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JESS Primer - Joint Expert Speciation System

1. iw hushed voice The labor of generations of architects and artisans hay been forgotten seeing only the perfection of the whole the result of giving ordinary human effort a direct purpose Science has ity cathedrals built by the efforty of a few architecty and of many workers such iy the edifice of thermodynamics G N Lewiy and M Randall cited by R E Mesmer inw Proc 5th Int Symp Hydrothermal Reactions pa Literature Reference System 1 THE LITERATURE REFERENCE SYSTEM This document tells you how to access the information in a JESS literature database JESS provides many facilities for processing such data but the description here is limited to the way you can inspect an already existing compilation INTRODUCTION TO JLR The JESS Literature Reference system called Knowledge is power JLR provides a powerful and versatile means and the computer is of storing and retrieving literature reference the amplifier of that power information EA Feigenbaum 1980 In general one tends to remember only one or two particular details about any literature reference One may recall the journal in which it was published or the name of the senior author or some aspect of the subject matter however one does not recollect everything nor even any single thing consistently The chief disadvantage of traditional methods of keeping track of the literature such as card indexes is that the collected data can be
2. Joint Expert Speciation System A powerful research tool for modelling chemical speciation in complex environments Peter M May Darren Rowland Murdoch University Western Australia and Kevin Murray Insight Modelling Services Pretoria South Africa JESS Primer Nda Red is positive aggressive and exciting It is the colour of the material the near the full blooded Bright red is stimulating and in general pleasing JJJJJ JJJJ EEEEER EEEE EEEEE SSSSS SSSSS SSSSS SSSSS SSSSS SSSSS JOINT EXPERT SPECIATION SYSTEM A joint venture by Peter M May Darren Rowland Chemistry Murdoch University Murdoch Western Australia 6150 and Kevin Murray Insight Modelling Services Pretoria South Africa A man would accomplish nothing if he waited till he could do it so well that no one could find fault with it Cardinal John Henry Newman 1801 1890 Please inform the authors of any errors or omissions in this manual Suggestions as to how it may be improved in any way are welcome Copyright Reserved February 2014 The JESS project is dedicated to Professor Peter W Linder who introduced us instructed us and inspired us We hope our work reflects at least some of his commonsense his scientific method and his liberal philosophy Acknowledgements The authors are indebted to the many people who have contributed to the JESS project in word or deed We especial
3. Literature Reference System 8 ABBREVIATION RULES It is generally possible for you to specify an item of data without having to type it in full Instead you only have to enter an abbreviation formulated in one of the following ways Abbreviations for References Reference identifiers can be abbreviated simply by leaving off a trailing part of the identifier In the limit only the publication name and the year of publication have to be entered For example the reference Talanta 1985 32 483 can be selected by entering the partial specifications Tal 85 or Tal 85 32 instead of and as well as the full identifier If you enter an abbreviation that matches more than one reference a menu will be displayed and you will be asked to select the particular reference you require Other Abbreviations Other data items namely author names publications and keywords can also be abbreviated In these cases the rules are i that any trailing part of the name may be omitted ii only those names which match the pattern of uppercase letters supplied are considered lowercase letters and punctuation symbols can thus be omitted from the given abbreviation For example the abbreviation EM would match the keyword Empirical Methods whilst EC would match Equilibrium Constant Usually if more than one existing item matches a supplied abbreviation the various possibilities are displayed on a menu and you are told to resolve the ambiguity by selec
4. tells you how to run JESS programs and briefly outlines how you should interact with them in general e THE THERMODYNAMIC DATABASE describes how you can inspect thermodynamic information using program VEWJTH THE LITERATURE REFERENCE SYSTEM describes how you can inspect the information in a JESS Literature database using program VEWJLR e FILE MANAGEMENT describes how you use your computer s operating system to organize and store your files TEXT EDITING describes how you can prepare and edit data for input to JESS programs using the JED text editor e JESS MODELLING FACILITIES provides a short summary of the major capabilities of JESS for modelling chemical speciation EQUILIBRIUM CALCULATIONS describes how you can perform a simple calculation of an equilibrium distribution using the sequence of GEM programs WHAT NEXT suggests ways in which you extend your knowledge and use of JESS SUPPLEMENTS describe how you can access physicochemical property information using program WEWFIZ or solubility data using program VEWSOL Most of us are so keen to try out a new software package that we are tempted to try it without first digesting the documentation After all we ve just gone to considerable expense to obtain it or we ve just been told that it can solve our most pressing problem We want results Then we hit a problem and at best denounce the package as not user friendly Accordin
5. A variety of JESS modelling facilities are available that automatically utilize the data provided by FIZ These include optimisation programs which determine the model parameters by least squares regression and simulation programs which use the parameters so obtained to calculate physicochemical property values under specified conditions of temperature pressure and concentration Three main theoretical frameworks have been implemented one based on the Pitzer equations another on the H ckel equation and a third on Zdanovskii s rule for multicomponent solution mixtures It is possible to display FIZ database values raw and modelled with corresponding graphs in Excel spreadsheets Consult program HELPER for instructions on how to install this powerful facility Work has commenced on the development of another physicochemical database focussed on solubilities called SOL This is more general than FIZ but necessarily more cumbersome You can inspect the prototype SOL database using program VEWSOL CHEMICAL FACILITIES These programs include CHMUTL to convert concentration units to provide information from the periodic table and to calculate molecular masses FCCUTL to calculate activity coefficients using various extended Debye Hiickel models and to correct equilibrium constants for the effects of ionic strength or temperature change TSTH2O to calculate various physicochemical properties of water and PEPTID to determine the mole
6. Na C104 449 Calcium Sulfate Gypsum Solubility in NaCl Soln 454 Calcium Sulfate Gypsum Solubility in H C104 Soln 463 Calcium Sulfate Gypsum Potassium Sulfate Solubil 464 Calcium Sulfate Gypsum Potassium Sulfate Solubil 465 Calcium Sulfate Gypsum Potassium Sulfate Solubil 466 Calcium Sulfate Gypsum Potassium Sulfate Solubil 467 Potassium Sulfate Calcium Sulfate Gypsum Water 479 Calcium Sulfate Gypsum Solubility in Water e Then have your selected set of data displayed SOL Command H L Q S U V lt L gt V TXT file name OR dataset number 435 Dataset 435 Calcium Sulfate Gypsum Solubility in MgC12 24192 Analytes Ca 2_SO04 2 Mg 2_C1 1 2 VBS Cl 1 Ca 2 S04 2 Mg 2 Wgt 5p Press 1 0 atm Temp 35 0 C CACLMG Concl Conc2 ADens FIZDA FIZ_SV FIZ_KY Phase line m m 38 0 0551 0 34 1 030 1030 1564 39743 Ca 2_SO04 2_H20 2 _ s 39 0 0611 0 68 1 053 1053 1594 374 1 Cat 2_SO4 2_H20 2 _ s The Solubility Database 3 24192 gives the JLR literature reference number of the data source Analytes refer to the chemical entities whose total concentrations determine the composition of the solution VBS refers to the Variable Basis Species which should be used as a basis set for calculating the chemical speciation of the solution CACLMG is the name of the text file containing this set of data ADens refers to the Analytical Density the solutio
7. The Thermodynamic Database 5 Select the first item in the menu Select one 1 7 lt 1 gt 1 Species Gly 1 Cu 2 H 1 Here again spacing is important Blank spaces surround the plus signs separating the species symbols What sort of display Full lt Brief gt Quit ENTER All the located reactions should thus be displayed You could note the corresponding reaction numbers and later display the associated thermodynamic data using the view data command sequence shown at the beginning of this example for reaction number 1 To return to the JTH command prompt you must enter Q for Quit Now you can try another kind of search Species B The B stands for Back its purpose is to return the prompt before the current one this is a standard JTH command which works at many prompts Here it should cause the locate menu to be redisplayed Choose option 5 Species with given name fragment Select one 1 7 lt 1 gt 5 Chemical Name or Synonym proton The program should then show the species symbol H 1 for the proton Chemical Name or Synonym water The program should now show the species symbol H2O for water and perhaps for other compounds whose name contains water Terminate execution Chemical Name or Synonym Q JTH Command H L Q V lt L gt Q Confirm Quit lt Yes gt Y The Thermodynamic Database 6 BROWSING THROUGH THE DATABASE You can browse through the database using a con
8. You can enter Modify mode from line editing mode by enter the command Modify followed by a two numbers separated by a colon to indicate the range of lines that should be loaded into the modify buffer You terminate Modify mode by entering the command Quit which can be abbreviated to Q To terminate modify mode without implementing any changes enter QIU for Quit and Undo Text editing 6 How not to get lost in the complexities of our own making is still computing s core challenge Edsger Dijkstra 1990 cited in User Interface Design by H Thimbleby Modelling Facilities 1 MODELLING FACILITIES This document describes in general terms the modelling capabilities of JESS It is intended to give you an overall perspective before you read the EQUILIBRIUM CALCULATIONS document in this Primer or plunge into the business of modelling itself PLEASE NOTE JESS distributions nowadays do not include the kinetic modelling facilities Contact PMM if you want this capability JESS RAISON D ETRE JESS is a computer system for determining chemical speciation in complex aqueous environments The JESS concept came from a union of two main ideas first that chemical speciation has many significant and varied applications across a wide range of O world invisible we view thee scientific disciplines and secondly that this O world intangible we touch thee potential is largely unfulfilled because of O worl
9. at the prompt in question to have this displayed You can also use program HELPER to obtain advice about specific subjects Information is provided about topics programs and events At the prompt you either enter one or more keywords of interest to you or you enter a label to display the particular help text associated with a given topic Keywords recognised by program HELPER can be any word or phrase that you can think of in connection with the area in which you are needing help You can enter more than one keyword simultaneously separated from each other by for inclusion or for exclusion Thus view database literature finds entries associated with inspecting databases other than literature databases Labels have the form xmny where x and y are alphabetic letters and m and n are digits They are displayed alongside the index entries located when you enter recognised keywords Simply type any label at the prompt to have the text displayed for the topic concerned Equilibrium Calculations 2 A WORKED EXAMPLE Position yourself in an empty directory folder It is important to do this because it ensures that no matter what happens you will not affect anything except the temporary files created during this exercise At the end of this worked example you will delete everything in your working directory folder to leave this exactly as you started Moreover if something does go wrong you can alway
10. family names comprising more than one word are typed as such ii Initials again capitalised as required are placed next separated from the family name by a blank space no spaces or periods may be included in the string of initials but other punctuation is acceptable as necessary iii Authors can be entered in an abbreviated form as described later Examples of typical author names are Watson JD Crick FHC Bragg W_Jr van der Merwe KJ Conference Management Committee Literature Reference System 7 Publications Book names are generally stored in full journal names are stored in the form recommended by IUPAC Both can be abbreviated by you as described later Examples of typical publications are Talanta J Chem Soc Dalton Trans Light Metals Sov J Non Ferrous Metals Tsvet Metall Keywords Keywords are stored in full Examples of typical keywords are Speciation Distribution Redox Reactions Transition Metals Equilibrium Constants Iron Natural Waters Cross References References can be associated with one another This is useful in some particular but fairly infrequent circumstances In the JPD thermodynamic database they are used to indicate either that the same literature article appears as two or more references as when it is published in different languages or that the publications deal with the same thermodynamic data You are advised not to worry about this until you have more experience
11. manager and text formatter We even have programs to code and decode text files for transmission across electronic networks JESS is so to speak a system for all seasons a system designed to be flexible and varied in its applications By now you probably think we are the world record holders for wheel re invention Indeed we are often so condemned especially by the computer science fraternity This is not the place to defend our policy in detail perhaps one day we can discuss it over coffee or better still over something stronger Suffice it to say that by developing a broad spectrum of facilities for ourselves we have ensured a that JESS can be ported readily to different computer systems especially to those of the future b that our data can be manipulated efficiently and accessed in the way we require and c that our system was as free as possible from various other conceivable constraints What seems important to us in the present context is that whilst you familiarise yourself with JESS you explore beyond its standard applications looking for others that may also be useful to you We trust that as your experience grows you will find the system becomes progressively more powerful Good luck and Bon Voyage Nia Joint Expert Speciation System A powerful research tool for modelling chemical speciation in complex environments Peter M May Darren Rowland Murdoch University Western Australia and Kevin M
12. string abc Other searching capabilities are described in the JESS User s Manual You can exchange occurrences of specified text in your file with other text using the Substitute command which can be abbreviated to S For example S labelwxyzl will replace every occurrence of abc with wxyz You can cancel the effect of previous commands using the Undo command which can be abbreviated to U You can terminate your editing session without having any changes implemented by entering QIU for Quit and Undo Text Editing 5 Modify Mode This is indicated by the prompt spread over two lines Mod Cmd gt The lines of text are held in a special buffer and are referenced by position i e not by line number Modify mode is commonly used by the programs that prepare input for your speciation calculations Enter a period to move to the first line in the buffer enter an asterisk to move to the last line in the buffer press IENTERI to move to the next line in the buffer if there is one e The commands for Back Copy Delete and View without line numbers have the name function as they do in line editing mode Lines can be edited in Modify mode using the same conventions of characters typed under the current line as described under line editing mode You can enter Modify mode from Text accepting or Input mode by entering the command Modify which can be abbreviated to M
13. which you should already have consulted You also need to be familiar with the jed editor as described in the TEXT EDITING document You will find JESS modelling unlike any that you may have experienced previously Indeed you should expect it to take some time to adjust Remember that the decision The old order changeth making process entailed in every yielding place to new equilibrium calculation is subtle and And God fulfils Himself frequently much more complicated that it in many ways seems JESS will guide you through these Lest one good custom issues but in doing so will make a large should corrupt the world number of assumptions about your modelling context This is appropriate Morte d Arthur initially whilst you are learning However by Alfred Tennyson 1809 1892 subsequently it is your responsibility to ensure that the answers you are getting in fact apply to the questions you want to ask It is also important to appreciate that the description of the JESS equilibrium calculation facilities given below is not and cannot be comprehensive The object for now is simply to get you going As and when specific issues arise during your modelling activities you should consult the on line documentation for more detailed information With the programs used to prepare your input for equilibrium calculations most prompts have additional text available describing what is required simply type H for Help
14. Delimited ASCH files 2 D species distributions Contour plots GEM INTERFACE QUICK REFERENCE GUIDE cont execute a Modify lgK of a species directly TELQED Modify IgK of a species by modifying entries in UPDJTH the thermodynamic database Change T and I ranges over which IgK correction TELLGK functions best apply and execute programs onwards from DOQED DOQED DOLGK select species and select prevent species form being considered option select species and specify a single overriding lgK or one more other UCC parameters select database DBA change the reaction data as required execute program UPDUCC check UCCs are appropriately modified e g using program UPDJTH modify conditions for maximum reliability DOLGK TELQED Remove a variable basis species from the model Add or remove solids at the QED stage TELQED modify the list of solids DOQED TELQED select Advanced Facilities and invoke charge balance also DOQED reduce by one the no of concentrations specified Apply the charge balance equation Override internal JESS initial estimates e g to TELQED deal with computational overflows Use results of a previous DOQED as initial TELQED estimates for the current run specify a log fixed free conc for the species 1000 DOQED select Advanced Facilities and Initial Estimates and specify required values DOQED DOQED select Advanced Fac
15. Primer During this introduction it is important that you explore adventurously Don t worry about your inexperience you can t do any damage The programs chosen to demonstrate JESS are for display and calculation purposes only They do Don t worry be happy not alter anything permanently OTHER JESS FACILITIES The purpose of the Primer is to introduce you to the facilities encountered most often by the average person using the system The programs mentioned are only a few amongst more than 350 in the JESS package Clearly there will be further applications of JESS beyond those dealt with in the Primer awaiting you However you should note that many JESS programs were written for use only by us the developers of the system They are not needed to perform speciation calculations nor are they involved in the processing of data required for such calculations Details of these other facilities are given in the Developer s Manual Another useful facility is the JESS website http jess murdoch edu au This allows you to inspect out databases over the internet albeit in rather restricted ways and it also provides certain help documentation on topics beyond those covered in this Primer INSTALLING THE SYSTEM As far as this Primer is concerned JESS should already be installed on your computer and you should know how to access it If these assumptions are incorrect you must either install the system yourself or o
16. Species with a given name fragment The symbols of all the species primitive or composite are displayed that have a name which matches the set or sets of characters you enter As above you can define the search more precisely by entering more than one set of characters separated by or for inclusion and exclusion respectively Alphabetic casing is not significant The name fragment s you specify can occur anywhere in the name of the species i e not just at the start c f searching for names using the Query facility To focus the search it is a good idea to be as specific as possible For example entering eth diam tetra acet acid is much more informative than entering just eth diam or tetra acid It is better to use short name fragments which you are certain will occur in the name exactly as you enter them rather than longer strings which may not match because of differences in punctuation etc Thus you should enter meth rather than methylene Organic chemical nomenclature unfortunately is not as systematic in practice as in theory Beware especially of the positional numbering in names i e do not assume that the numbers occur in the name where you think they should On the other hand specifying positional numbers by themselves as a separate included name fragment will often narrow your search very helpfully The Thermodynamic Database 12 INFORMATION AT ANY TIME At odd times and places you may wish to check some
17. appropriate Note that in the representation of a chemical equation as just described the signs must always be surrounded by blank spaces This permits the database programs to distinguish the species occurring in the reaction and not to be confused by the signs of electronic charge which occur in species symbols Consider the JESS format for reactions used in the following examples H 1 OH 1 H20 Cu 2 2 lt OH 1 gt Cu 2_OH 1 2 Here H 1 OH 1 H2O and Cu 2 are primitive symbols and Cu 2_OH 1 2 is a composite symbol Note how the non unit stoichiometry is dealt with using angle brackets and parentheses Some other rules for representing reactions are indicated in the following diagram species enclosed in lt gt if preceded by a coefficient reactants separated from products by note spaces water included to achieve y complete mass balance Fe 3 3 lt OH 1 gt FeOOH alphays H2O real or integer coefficient plus or minus signs surrounded by blanks Note the way the phase is specified in the species symbol for solid FeOOH Solid phases always end with an s inside the parentheses individual polymorphs may or may not be indicated as in Mn gamma s or Mn s respectively Clearly this way of specifying reactions requires a lot of care and entering many reactions as described above would be tedious Unlike the species symbols the representation or reactions cannot be truncated Fortunately there are other
18. aware of all the factors on which these decisions ought to be based especially initially Hence it is difficult for inexpert users to specify precisely how to model the chemical system of interest to them Instead this expertise must be provided by JESS with the computer making whatever choices seem best to suit your Modelling Facilities 4 circumstances In this sense every expert system necessarily has to be something of a black box Of course we the developers of JESS do not want the criteria used by our software to remain forever hidden from you On the contrary we believe that equilibrium calculations in which the methods and assumptions have not all been made absolutely explicit should be firmly rejected Indeed you will find yourself frustrated from time to time when JESS faithfully reminds you of the effects of some earlier decision you have made or was made for you As tedious as this may seem when it happens it is better than the alternatives hiding or ignoring these decisive issues To us then the matter is simply one of order if JESS can produce results by making as many sensible decisions itself as possible you can initially restrict yourself only to those which are critical to your application In most cases these specific issues will be relatively few in number and even more to the point are most likely to come into focus only when you inspect the results of your modelling You are then in the best position
19. conventions used to control and work JESS Most people find this harder at first but succeed with a little patience and perseverance Once they become familiar command driven systems are much more powerful and efficient than their graphical alternatives To begin you should establish two things 1 The form of instruction required by the operating system to execute the program In a standard JESS environment for stand alone programs you enter XQT program name Under the Windows operating system you need to work in a DOS window We recommend a a buffer size of 50 and b a screen size of 8 x 12 be set up as defaults 2 You are correctly positioned to access the JESS computer files that you require Typically files reside in directories or folders i e named areas of storage which may hold many files JESS programs have specific requirements concerning the directories in which their data files are located You may or may not be aware of the files that you will use and or their location More details are given in the JESS Developer s Manual You will only be concerned with this if your working environment on the computer has not been properly set up Getting Started 2 RESPONDING TO JESS PROGRAMS Most JESS programs are interactive This means that you communicate with the program while it is executing You provide information when prompted and you give it commands to perform various tasks This does
20. gt NO Y Note that in this example all responses were entered explicitly i e defaults were not used In practice you would normally just press ENTERI when the default displayed by the program was in fact the option you wanted This was the case for instance on the first occasion that the JLR command prompt appeared the default response lt V gt could have been invoked Also note that in practice one rarely needs to type out responses such as the author name in full You could for example abbreviate by entering just the uppercase letters i e BGN for Bloggs GN Try the example again This time use default responses where appropriate and abbreviate the author name Remember to enter Q for Quit if you get into any difficulty BROWSING THROUGH THE DATABASE For convenience it is possible to use a special convention to specify reference numbers without typing them out in full By entering certain special symbols the program can be made to display references on either side of the one last shown or to display the reference last entered into the database The symbols are as follows Symbol Meanin lt Reference number one less than that just shown gt Reference number one more than that just shown The last reference Using this mechanism you can easily and rapidly scan through a sequential series of references using just one keystroke to display each one Beginning at the JLR Command stage one presses the ENTERI key to
21. in your current working directory folder Note that a special link must exist at operating system level so that the programs can find this directory folder as described in the instructions for implementation and the file protection mechanism must permit at least read access to both the directory folder and the files therein If you do not know how to establish the above or it doesn t seem to help you need assistance Ask whoever was responsible for installing JESS on your computer or if that happens to be yourself contact Peter May may murdoch edu au Getting Started 4 J the days when everybody started fair Best Beloved Va MESES a sy 22 D f This is the Wise Baviaan the dog headed Baboon who is Quite the Wisest Animal in All South Africa 4 Ta ww ta OnT Jant ii boy ax T8838 DATA Not always was the Yangaroo as now we do behold him but a Different Animal with four short legs Some excerpts of joint interest from Just So Stories For Little Children by Rudyard Kipling 1865 1936 The Thermodynamic Database 1 THE THERMODYNAMIC DATABASE This document tells you how to access the information in a JESS thermodynamic database JESS provides many facilities for processing such data but the description here is limited to the way you can inspect an already existing compilation INTRODUCTION TO JTH Th
22. should restrict yourself to the simple task of specifying the concentrations required to perform a single equilibrium calculation but later you ll discover that by using the Scan facility you can process a large equilibrium space very conveniently The concentrations you specify fall into two categories fixed free concentrations and total concentrations Usually you will wish to have the species H20 H 1 and e 1 in as fixed free concentrations Note that in all contexts you are likely to be concerned with for some while at least unity should be specified as the concentration for H2O The concentration for H 1 is that corresponding to the solution pH i e log H The concentration for e 1 is that corresponding to the redox potential of the solution i e say log e 5 for mildly reducing conditions and 5 for mildly oxidizing conditions Your other basis species will generally be specified in terms of their total concentrations Check carefully that the number of concentrations you give overall i e as totals and as fixed frees is the same as the number of basis species which you have Otherwise the equilibrium calculation will fail because the number of equations and the number of unknowns do not match Use the V for View option on the QED Command prompt to display a summary of the input you have specified and check that this seems OK before quitting TELQED Execute program DOQED and VEWQED Follow the VEWQE
23. sorted and maintained in order of only one of these various kinds of information The JLR computer system is designed to store many literature references ina way that permits them to be found even when recollections about them are quite vague Our approach to the storage and manipulation of literature references differs from that of many other literature database systems in that the items associated with each reference such as the author names keywords and publications books and journals are treated specifically and not just as character strings in different database fields This means that it is easier to avoid errors due to slight and often insignificant differences in the way the item is entered In particular JLR uses a method of abbreviation which helps you to pick out the item in question without having to type the whole character string The most important use of the JLR subsystem within JESS is to support the management of the literature references associated with our thermodynamic data especially in respect of the JESS Parent Database JPD Details on how to access the JTH subsystem are given in the document in this Primer called THE THERMODYNAMIC DATABASE On the other hand the JLR facilities are entirely independent of JTH Some users of JESS software are only interested in JLR Although the description of JLR provided here deals mostly with how you inspect an already existing database you should be aware of the other facilities
24. then proton In a three component system the digits refer in order to metal ligand and proton In a four component system the metal comes first then the primary ligand then the secondary ligand and the proton last Proton stoichiometric coefficients can be negative For example by entering you specify the reaction B110 M L ML B012 L H LH B12 L H LHO B22 2 2 lt M gt 2 lt L gt 2H20 M 2 _L 2 _OH 2 2 lt H gt B1210 M 2 lt L gt X ML 2 _X The initial letter B serves to distinguish these stoichiometries from a reaction number In the second method the letters M L X H and the pair OH are used to identify components The reaction is specified by formulating an expression for its equilibrium constant species are represented by combinations of these letters with digits giving the stoichiometry separated by a period for multiplication of species concentration or by a slash for division Thus for example by entering you specify the reaction ML M L M L ML LH L H L H LH LH2 L H2 L 2 lt H gt L_H LH2 LH H LH H LH M2L2 OH 2 H2 M2 L2 2 lt M gt 2 lt L gt 2H20 M 2 _L 2 _OH 2 2 lt H gt ML2X M L2 X M 2 lt L gt X M L 2 X The Thermodynamic Database 9 Clearly it is easier to use the beta mechanism if it is applicable Note however that the main saving achieved by both methods is that 1 symbols do not need to be typed at length and ii the variety of symbols and spa
25. to consider the decisions that led to your particular outcome Typically you will wish to change one or more of them and redo your calculation How you go about making such changes is described next and in the EQUILIBRIUM CALCULATIONS document Why are so many computer programs needed for an equilibrium calculation All equilibrium calculations performed by JESS are divided into a sequence of small ish steps Each step is implemented by a separate program and each step also has programs dealing with input and output at that step When you wish to alter something about the calculation you just need to identify the point at which the decision in question was taken It is then a relatively straightforward matter to change the input at that step on which the decision was based and to repeat the calculation from that point onwards In practice then you initially perform each of the necessary steps in your equilibrium calculation automatically Apart from specifying some basic information about the chemical system you wish to model you do not concern yourself with the means by which the computer makes decisions as you go JESS provides this input by default In this way you rapidly accomplish an initial calculation and you successfully obtain a speciation distribution Typically you will then notice in your results something unexpected or unwanted For example you may be surprised that no solids have appeared because by default precipit
26. ways of doing things so you will rarely need to construct these reaction specifications in full The Thermodynamic Database 8 Abbreviating chemical reactions The simplest way to specify a reaction is to enter its number if you know it All reactions in the database are assigned a unique number which can be entered at any prompt where a reaction is required In addition there are two abbreviated methods of entering a JTH reaction Neither are entirely general but they can be used to specify many reactions in a quick and easy way Both abbreviated methods depend on a preliminary identification of the reactants in terms of a metal ion and one or two ligands One ligand called the primary ligand must always be specified In the first instance you will be prompted automatically for this information Thereafter identification of reactants can be changed by appending an exclamation mark when you enter the abbreviations The first method applies when the reaction is written as a formation reaction i e where the product is a single complex and the reactants are the individual unassociated components of the complex For example if the reaction can be written as X Y X_Y then X_Y is said to be the complex and X Y are its components The reaction is then specified simply by a B for beta followed by a string of digits that give the stoichiometry of the complex In a two component system i e with two digits the order is ligand first
27. you have entered them correctly and that they are in the database you are using The program should then show the thermodynamic data for the reaction 3 lt Gly 1 gt Ni 2 Ni 2_Gly 1 3 Achieve the same output in another way Reaction ML3 M L3 The program should immediately redisplay the data shown above Note that you do not have to repeat the identification of the metal ion and ligand these continue to be assumed until you explicitly change them The easiest way to make such a change is to append an exclamation mark after the reaction abbreviation You will then again be prompted for the species symbols The Thermodynamic Database 4 Try this remembering that casing is not significant in JTH Reaction B120 Symbol for M metal ion lt Ni 2 gt Cu 2 Symbol for L primary ligand lt Gly 1 gt Select the default response Enter Gly 1 to the above prompt simply by pressing IENTERI This should now evoke the thermodynamic data for 2 lt Gly 1 gt Cu 2 Cu 2_Gly 1 2 Now try examining the data for glycine protonation Reaction B12 and Reaction LH2 L H2 have the same effect showing the overall reaction whereas Reaction B11 gives the first proton association constants and Reaction LH2 LH H gives values for the second Now try something else Reaction Q JTH Command H L Q V lt V gt L Locate all the reactions involving glycine copper ions and protons for example
28. Apparent Molar Enthalpy of Mixing kJ mol HM Apparent Molar Enthalpy of Solution kJ mol HS Molar Excess Enthalpy kJ mol HX Isopiestic HSO Concentration m IA Isopiestic CaCl Concentration m IC Isopiestic LiCl Concentration m IL Isopiestic MgCl Concentration m IM Isopiestic KNO3 Concentration m IN Isopiestic KC Concentration m IP Isopiestic NaCl Concentration m IS Isothermal Compressibility GPa KI Apparent Molar T Compressibility cm mol bar KT Apparent Molar S Compressibility cm mol bar KS Isentropic Compressibility GPa KY Osmotic Coefficient unitless OC Osmotic Pressure Pa OP Partial Molar Solvent Heat Capacity J K mol PB Partial Molar Solute Heat Capacity J K mol PC Harned Cell Potential Difference V PD pe unitless PE Concentration Cell Potential Difference V PG pH unitless PH The Physicochemical Property Database 7 Partial Molar Solute Enthalpy kJ mol PQ Partial Vapour Pressure Pa PP Partial Molar Solvent Enthalpy kJ mol PR Partial Molar Solute Entropy J K mol PS Partial Molar Solvent Entropy J K mol PT Partial Molar Solute Volume cm3 mol PV Partial Molar Solvent Volume cm3 mol PW Sound Velocity Difference cm sec SD Solubility Saturation Limit m SL Sound Velocity m sec SV Molar Excess Entropy J K mol SX Specific Volume cm3 g VD Apparent Molar Volume cm3 mol VM Vapour Pressure Pa VP Molar Excess Volume cm3 mol VX Standard Molar Volume Offset cm3 mol VZ Instructions on how to implement the 8 ball fa
29. CUMENTATION A limited amount of information is available on line if you have access to the whole of JESS Specific parts of this documentation are displayed when you enter the Help command at the relevant prompts of many JESS programs In addition you may browse through the help material and search for text associated with certain combinations of keywords using the program HELPER The information available through program HELPER is organized into sections each of which is located by a label i e a distinguishing sequence of alphanumeric characters such as TO1A You use the index facility of program HELPER to find out what these labels are By entering keywords for subject of interest to you you can obtain a list of index entries each with an associated label Then to read the help text you want simply enter any label chosen from the displayed list WHAT TO DO IF YOU HIT A PROBLEM WITH INSTALLATION If you have any difficulty getting started it will almost certainly be because your instructions have been deficient and you are not set up correctly It is then a good idea to go through the instructions again carefully to see where you might have been misled If this doesn t help you should try a little investigation to unearth what has gone wrong Most problems experienced by newcomers to JESS can be traced back to one of three causes a Your JESS licence is invalid or being implemented incorrectly Make sure your JESS usernam
30. D procedure just as in the worked example at the start of this document Equilibrium Calculations 10 MODIFYING YOUR THERMODYNAMIC INPUT DATA In the development of most models the first calculations you perform will be based entirely on the data which comes from JPD the JESS Parent Database This information is extracted during the SUB stage during which all the relevant data is transferred from JPD to a sub database in your working directory folder this sub database is called DBA by default It is only the contents of your sub database that are processed by the LGK and subsequent programs Should you need either to introduce new thermodynamic data or to modify existing values you do so by modifying your sub database For this typically you use program UPDJTH You inspect the data using UPDJTH in exactly the same way as you did with program VEWJTH as described in the THERMODYNAMIC DATABASE document of this Primer Entering new equilibrium constants should also be relatively straightforward simply identify the reaction in question and provide the information requested at the prompts that follow the successive commands Insert and Data How to insert new reactions or more problematically new species is described in the on line documentation which can be accessed by program HELPER however both of these advanced manoeuvres are probably best avoided until you have gained some experience in using JESS Importantly you should
31. E NEXT SUPPLEMENT PHYSICOCHEMICAL PROPERTIES 1659 OPENING UP THE BLACK BOX Approaching JESS 1 APPROACHING JESS Welcome We the authors of JESS extend greetings to you May your journey with us be a rewarding one WHAT JESS CAN DO FOR YOU Inside every large program there is a little program trying to get out JESS is a large body of computer software concerned primarily with the modelling of chemical phenomena in solution Although the package has many aspects to it a strong emphasis is placed on the concept of chemical speciation i e the identity and relative abundance of different chemical entities which may occur in a system Hare s Law of Computerdom Some JESS statistics 377 programs Speciation is important because it often 312 000 lines of code controls the properties of chemical systems The behaviour of many biological environmental and industrial processes depends on the concentration of individual species These concentrations arise from the thermodynamic equilibria and kinetics of competitive reactions Knowing only the total amount of each element in contrast is 26 100 literature references Thermodynamic database 76 400 reactions 248 000 constants Physicochemical database 404 000 values 678 solutes much less useful than is commonly supposed JESS contains a great deal of coded knowledge about chemical speciation and about the way chemical speciation calcu
32. EF for references each of these three letter codes can be shortened to their first character abbreviation represents any valid abbreviation as described above Note that the blank space between the question mark and the code can be omitted but that the space between the code and the abbreviation cannot e g P Tal performs the same search for Talanta as PUB Tal In order to scan through the list of existing entries without having to formulate abbreviations to match those items which are present the query facility displays the first ten items following the first match found rather than just those fitting the given abbreviation Once a match has been found you can list all following items by repeatedly entering P K etc i e omitting the abbreviation DATABASE MANIPULATIONS In addition to VEWJLR there are many other JLR programs Most of these are used for building Literature Reference databases The insertion of new reference entries and their alteration if necessary is performed using UPDJLR Database modification introduces a need for housekeeping i e the internal tidying which becomes necessary to maintain access efficiency For this purpose programs such as BLDJLR MNTJLR and DMTJLR are provided A useful JLR facility enables you to print out literature references in any desired format This can be useful when you are preparing a manuscript for publication This is accomplished by the program FMTJLR The instructions wh
33. Mini Models are application specific all the chemical relationships and most of the equilibrium data at least must be fixed in advance On the other hand whenever it is possible to identify a well defined speciation calculation a tailor made JESS Mini Model can be constructed to provide results with exceptional speed and accuracy Modelling Facilities 8 KINETIC CALCULATIONS JESS presently has two different kinetic facilities First it is possible to set up a purely kinetic model just based on differential equation solving The facility is similar in concept to that provided by most conventional simulation packages it allows you to define a set of differential equations and given the starting values to solve for changes occurring over time It is called the DE Differential Equation interface and like the GEM interface it involves a sequence of calculations ie the DE DES and DEO stages However the DE interface can be used without reference to any chemistry Secondly there is the KEM Kinetic and Equilibrium Modelling interface This allows both kinetic and equilibrium processes to be modelled simultaneously The chief advantage of this approach is that it accommodates systems with compartments in which the equilibria are too numerous or too complicated to be included directly in the differential equations being solved Based on JESS Mini Models the KEM sub system of JESS allows construction of models for very l
34. all the programs in the form of a Quick Reference Guide is given on the next page GEM INTERFACE QUICK REFERENCE GUIDE GEM STAGES Generalised Equilibrium Modelling SUB LGK BAS QED OUT Elements Primitive Conditions for Uncoupled basis species lists Scan info Fixed frees and totals Determinands required as Py DOl Source Meu Excluded primitives Included pons PAI and I peds w P output including those TEL and User database Reliability i ignored lgK s dH s and CP s to be Ka reactions Preferred Variable and the required by a future Mini Excluded Thermodynamic overridden initial estimates Charge Paper MBU Basis species Model Primitives Basis Species Order balance DO Create Sub Determine LGK Determine Variable and MBU Determine Quasi Equilibrium Calculate values of database Basis Set Basis species sets Distribution determinands l amp no determinands amp no Speed at ite Sein Fast Fast no scan points scan points and depends on primitives fhe Various Species yee ang NRU tanis Ss Speciation Phase distribution pup aan Lists Reaction Rea Hony toiming species Supersaturation Partial Pressures VEW statistics and containing a specified primitive P j f primitives Lists Basis sets and the Rogues gallery Unconditional Correction Coefficients lgK and dH Charge Balance Ionic Strength Data Quality
35. and Murray K Talanta 1991 38 1409 JESS was intended to deal specifically with these problems allowing users to determine speciation distributions easily efficiently and reproducibly Above all our objective is to eliminate progressively the various sources of error which always seem to impact on the traditional methods of calculation To achieve this goal it is obviously necessary for us to have a simple user interface even though the underlying decision making process is very complicated We have thus implemented the approach described above which initially requires as little input from you as possible You need to provide only the barest minimum of information about the chemical composition of your system JESS provides the rest as default input When you begin using JESS you will tend to change these defaults only when it becomes apparent that they are not what you want As your experience grows however you ll probably find a mixed mode of operation most convenient i e specifying the more obvious input parameters in advance only if this is required by your model of course and attending later to any matters that you initially overlooked or which have arisen unexpectedly from the outcome of your calculation There are five steps in the sequence that comprises a JESS equilibrium calculation We call these the GEM stages GEM stands for Generalized Equilibrium Modelling Everything that needs to be done to yield a speciation
36. arge and complicated chemical systems Such capabilities are essential if we are to solve many of today s most pressing problems in applied solution chemistry We think the potential benefits are considerable with exciting and varied industrial environmental and physiological potential Our chief hope is that as with your GEM calculations you will find that your kinetic modelling can also be done painlessly and without error MODELLING TECHNIQUES Chemical equilibrium models are deterministic i e from a given starting point the outcome of the model is always the same as predicted by the parameters and mathematical relationships of the model For this reason perhaps you may be expecting to obtain one specific and quantitative answer from your modelling calculations Sometimes it will be so but often matters will be less clear cut than this for a large number of reasons What is very important for beginners to realise is that chemical equilibrium modelling generally offers you much more than a particular distribution of chemical species To make the most of JESS you must go far beyond any single calculated result Your general purpose should always be to examine the extent that different chemical models behave as reasonable representations of the real life system Your knowledge of the real system will develop from the links that either appear or do not appear during such an investigation We like to encapsulate the essence of this approac
37. assist you in your chemical researches Thermodynamic Reaction Modelling In most JESS modelling the speciation is calculated using known thermodynamic parameters for the relevant reactions in aqueous media All types of chemical equilibria including protonation complex formation redox solubility and adsorption can be modelled Variations in the relative amounts of components ionic strength temperature and solution pH are fully taken into account The profile of all species is obtained regardless of how little of each one may be present The calculations are thus especially useful when systems are not amenable to experimental investigation either because they are too intricate or outside analytical range Indeed the models are at their most powerful when predicting the chemical behaviour of complex mixtures Since speciation models are thermodynamically based not empirical their results are always sound at least within the limits of the available thermodynamic data Thus the insight you can obtain from these models is governed only by expertise in assessing the accuracy and applicability of this data and by your imagination in probing the effects of the chemical relationships that operate in the system of interest to you However the limits of available thermodynamic data often make quantitative calculations problematic Modelling skills are needed to overcome or bypass the difficulties associated with poor or missing data Physicochemi
38. ates are not allowed to form Taking appropriate action to correct the unsatisfactory decision s in the calculation sequence is much easier once you have clearly identified a specific issue Good answers are rarely obtained without going through a number of these cycles Typically you ll discover a variety of factors which have an important bearing on the chemical system you are modelling It is these that are responsible for many of the difficulties with equilibrium calculations described at the start of this document Obviously they must be considered very carefully by you JESS can help identify the issues but for the most part only you can settle them You do this by thinking circumspectly about the chemical context of your calculation A key JESS facility in this regard is the record of methods and assumptions which is kept at each step in the calculation sequence You can inspect this record interactively and have it printed for Modelling Facilities 5 posterity Your final decisions recorded in this way whatever they may be should be retained in their entirety This is in case the basis of your modelling needs to be re examined later on You will soon learn that posterity often includes yourself and later may be surprisingly soon afterwards Why are kinetics involved in equilibrium calculations This is perhaps the most profound problem that JESS must help you to overcome It arises because most chemical systems regarded a
39. available for developing and modifying JLR data A brief outline of these can be found at the end of this document in the DATABASE MANIPULATIONS section Literature Reference System 2 A WORKED EXAMPLE Execute program VEWJLR It should respond as follows VEW JLR Version 8 2 Licensee Murdoch University Welcome Wednesday 17 Jul 13 15 50 JLR Command H L Q V lt V gt V VIEW Select the first reference Reference 1 This should evoke a display of the first reference entered into the database Usually the full reference is followed by details such as the authors the keywords the heading and the end page Note the name of an author For the purpose of this example say this is Bloggs GN Return to the top level of command Reference Q Then try the Locate function JLR Command H L Q V L Select to search by Author Type of search A K P C H Q lt A gt A Author Bloggs GN The program should locate Bloggs GN you should use the author name noted above If this fails you have almost certainly not entered the name exactly as it appeared above Capitalization is important here If more than one reference is found for the author you have chosen select a Brief display and if necessary page through the list thus displayed Type of search A K P C H Q lt A gt Q Literature Reference System 3 Terminate execution JLR Command H L Q V lt 1 gt Q Confirm QUIT lt YES
40. btain help from someone else who can do so JESS has been implemented on many computers and under many operating systems Note in particular that the JESS interface has been kept as simple as possible to maximize the number of computer environments that can support JESS now and in the future Detailed instructions on how to install the system are available Information sheets specific to your kind of computer should have been included with the material sent to you The corresponding MS Word files are distributed with this Primer on the JESS distribution CD ROM for Windows XP 7 Contact Peter May if you experience any difficulty Email inquiries can be sent to may murdoch edu au Getting Started 1 GETTING STARTED This document outlines what you need to know before attempting to use any JESS program Read it before trying anything RUNNING JESS PROGRAMS JESS consists of a suite of computer programs How you execute these necessarily depends on the computer system that you have available Since there are many possibilities we describe here what is required in principle You will need to adapt this to your particular situation This ought not to be difficult Thoughts are but dreams till their effects be tried Rape of Lucrece by William Shakespeare 1564 1593 All JESS operations are command driven as opposed to the point and click of a graphical interface This means you must learn the commands and
41. cal Property Modelling JESS also allows you to model a variety of physicochemical properties for electrolytes and a few non electrolytes in bulk aqueous solution Quantities such as activity coefficients osmotic coefficients relative enthalpies heat capacities and densities volumes can be calculated These models cover wide ranges of temperature pressure and solute concentrations typically to 300 C 1 kb and solute saturation Such modelling is based mainly on the well known Pitzer equations but other theoretical thermodynamic frameworks including the Hiickel equation and Zdanovskii s rule for electrolyte solution mixtures are supported There is a large underlying database comprising about 380 000 property values for over 500 solutes Far better an approximate answer to the right question which is often vague than an exact answer to the wrong question which can always be made precise Tukey s Principle cited by D D Perrin and R P Agarwal in Metal Ions in Biological Systems Vol 2 p 167 1973 Approaching JESS 3 ABOUT THIS PRIMER The purpose of this Primer is to guide newcomers in their initial approach to JESS It comprises a set of documents that tell you how to use the main JESS facilities These documents have been written as independently of one another as possible so that you can concentrate on those which are of most immediate interest to you The layout of the Primer is as follows GETTING STARTED
42. ch as carbonate Organic species if any are entered next under option 2 These are specified by their JTH primitive species symbols Ignore the Advanced Facilities option 3 When you are satisfied that your elements and species have been listed correctly return to the SUB Command prompt by entering Back or Quit instead of selecting a digit You may then obtain a summary of the input that is currently to be used for the SUB stage by entering the command View which can be abbreviated to V Finally terminate execution of TELSUB by entering Q and then confirming this with Y That completes your contribution to the SUB stage so you are now ready to have your sub database created Equilibrium Calculations 9 Execute program DOSUB After a short delay program DOSUB should report success You may then view a summary of what has been accomplished Execute program VEWSUB The subsequent GEM stages all have a similar approach However until you gain more experience there is no need to invoke either the TEL or the VEW programs until you reach the QED stage The following sequence is thus sufficient Execute program DOLGK Execute program DOBAS At the QED stage it is necessary for you to enter at least the concentrations of components in your model Execution of TELQED is therefore mandatory The necessary information is entered in the same sort of way as you did with TELSUB Execute program TELQED Initially you
43. cility within Excel spreadsheets can be found in Jess82 JesDoc Manuals Developers Excel Interface The Solubility Database 1 THE SOLUBILITY DATABASE This document describes how to access the information in the JESS Solubility database INTRODUCTION TO SOL The JESS Solubility Database stores the conditions of pressure temperature and composition under which solubility and other specified measurable properties of aqueous solutions have been quantified In particular the SOL system records physicochemical properties of many dissolved systems in terms of given overall concentrations of well defined substances in the aqueous phase When non aqueous phases exist in thermodynamic or metastable equilibrium with an aqueous solution these data define the regions of thermodynamic stability and hence the solubilities of each given phase When a thing is labeled complex that s just a roundabout way of saying you re not observant enough to understand it A Lee Martinez In the Company of Ogres Tor Books 2007 The general idea is to store literature data regarding thermodynamic properties of chemically reactive systems especially solubilities in a deliberately general way and to have a variety of computational mechanisms for finding and representing such data Chemical reactivity is the key feature that distinguishes SOL data from data stored in the FIZ database However to some limited extent the SOL and FIZ systems o
44. cing used in the full JTH reaction formulation is avoided The MLH mechanism has an additional advantage By employing it it is almost always possible to specify reactions using the conventions of Smith and Martell in their volumes of Critical Stability Constants These can be entered directly in the form they give Hence when considering a reaction from a Smith and Martell volume simply type the MLH abbreviation without regard to whether digits occur as superscripts or subscripts There are exceptions but this rule works in a very large majority of cases USING PROGRAM VEWJTH This program provides the so called read only facilities of the JTH package i e it enables you to examine and to search for thermodynamic data but not to do anything that would alter the database To begin the program prompts for the JTH database name If you are using the JESS Parent Database enter JPD After you have entered a valid name the program is command driven meaning that it expects you to enter one of several instructions indicating what you wish to do The prompt which is displayed when the program is waiting for one of these commands appears as follows JTH Command H L Q V lt V gt In response you can choose to enter any of the commands discussed below Each of them can be shortened to their initial letter The letter shown on the prompt between angle brackets which during the session is usually the previous command entered is the d
45. cular masses of peptides Three programs from the ESTA suite are also provided These are ESTAO ESTA1 and ESTA2b They are used to process potentiometric titration data as described in the ESTA publications ending with that in Talanta 1988 35 933 941 KINETIC MODELLING Some distributions of JESS also allow you to couple equilibrium to kinetic models Since kinetic phenomena depend heavily on the prevailing conditions and there is no body of fundamental data equivalent to that for chemical equilibria kinetic models tend to be much more limited than thermodynamic models in their predictive capabilities Nevertheless experience proves that the modelling exercise itself generally and frequently leads to new insight This is in part because model development effectively imposes a structure on one s thinking Models also help to identify the key factors amongst many which are known about the system In a manner analogous to the GEM stages and following on from them kinetic modelling is performed by JESS in three steps DEQ sets up a differential equation set KEQ builds a stand alone executable and KEM solves the differential equations to determine the changes in species concentrations within specified pools over time What Next 3 OTHER FACILITIES JESS also contains many facilities to assist with our everyday work on computers too many to mention all of them here We have our own English dictionary spelling checker thesaurus
46. d unknowable we know thee certain conceptual and technical difficulties in Inapprehensible we clutch thee calculating speciation distributions without error The Kingdom of God by Francis Thompson 1859 1907 The reasons for these difficulties are interesting but too complicated to deal with in much detail here Suffice it to say that problems abound which make the modelling of chemical systems highly demanding Indeed to determine correctly any but the simplest of speciation distributions requires an almost superhuman combination of expertise judgement and carefulness see J Chem Eng Data 2001 46 1035 for example It is therefore not surprising to find that many chemical models published in the literature are seriously flawed JESS is the outcome of an international effort to investigate and if possible to solve this problem The founding concept was to exploit progress in computer technology especially the well known but still spectacular improvements in hardware power and software methodology Many of our worries associated with chemical speciation modelling seemed amenable to a new computer based approach This remains as true now as it was then Our ongoing aim is to exploit the exactness and consistency of the computer and also to use the fact that much if not all of the necessary specialized knowledge could be encoded so that some artificial intelligence can be called upon to assist during the calculations Compu
47. d why we cannot cure the problem automatically are interesting but beyond the scope of this Primer They stem from the enormous range of thermodynamic stability of chemical species and the limited range and precision of numbers that can be processed by computers What is important to you is this a convergence failure can to our knowledge always be overcome if you manually take the necessary remedial action There are two main possibilities 1 When the convergence problem arises because of an overflow modify the initial estimates used by DOQED in solving the equations This is done under the Advanced Facilities option of program TELQED Typically you will need to identify one or more variable basis species associated with the problem and lower their initial value You do this by using program VEWQED to inspect the results of the failed calculation and finding those species associated with a numerical overflow The best factor to apply depends on circumstances e g smaller reductions tend to be necessary when the chemical species concerned has high stoichiometric coefficients Typically 15 will suffice but sometimes 25 or even 30 will be necessary 2 When the convergence problem arises because of an underflow modify the set of variable basis species using program TELBAS You need to find a set of basis species which at equilibrium will occur at reasonable concentrations say above 10 M You can guess the likely identit
48. detail regarding i chemical substance names ii background electrolytes iii solvents iv techniques by which a constant has been obtained or v weighting of data This can be done using the query facility Queries made in response to virtually any prompt take the form XXX abbreviation For example you can quickly establish whether chloride is recognized by entering NAM chloride In general the XXX used above indicates the type of list you wish to inspect and abbreviation represents any valid abbreviation for the item of data in question The letters XXX may be i NAM ii BEL iii SLV iv TEC or v WGT corresponding to the kind of data as described above Usually you will shorten these 3 letter codes to their initial character only Once a match has been found you can scan through all the following items in the list by repeatedly entering N B etc i e omitting the abbreviation Note that abbreviations in JTH are simply the initial characters of the item They are not case sensitive You must however enter the initial characters of the item exactly as they occur in the list to obtain a match this includes any punctuation and positional numbering in chemical names If you are unsure of how a chemical name occurs in the database but know roughly what it is you should use the LOCATE command option 5 DATABASE MANIPULATIONS Although we supply large amounts of data as part of the JESS package you may di
49. distribution and to formulate the kind of output you require is included All you have to do is to execute the sequence of GEM programs as described in the document on EQUILIBRIUM CALCULATIONS JESS MINI MODELS The capabilities of the GEM Generalized Equilibrium Modelling interface described in the preceding section have been accomplished at the cost of speed Those familiar with other computer programs that perform speciation calculations may well feel that the JESS approach takes longer and is rather more involved This is the price that must be paid for having a database that represents the thermodynamic literature in its original raw state as described above Fortunately once the difficulties of constructing a chemical speciation model have been overcome JESS makes it possible to abstract the specific equilibrium calculation Thereafter the speciation is calculated very efficiently as a function of the system s overall concentrations This is accomplished by special programs that produce a complete stand alone FORTRAN code for the particular chemical equilibrium model which has been formulated We call these FORTRAN codes JESS Mini Models For horrid commercial reasons the means of developing Mini Models are not normally made available to general users of JESS However you should be aware of them so that you can ask for a Mini Model when the need arises Perhaps the most important thing to remember is that
50. e and licence checksum are exactly as supplied These must be made available to JESS programs by the operating system typically via so called environment variables You can check that this data is properly presented to JESS using program TSTSYS b Your current working directory folder does not contain one or more of the data files required by the program you wish to run There are nine files in a Literature reference database AUT BUP FER KEY PUB QAL REF TUA and YEK with a KEY or K extension and at least seven files in a Thermodynamic database e g DBACPS DBAMOL DBANAM DBARXN DBASPC DBAYSA DBAZRA each with an IND or I extension The first three letters of the thermodynamic database files DBA in the example constitute the database name This database name is required when you execute VEWJTH as described in the document THE THERMODYNAMIC DATABASE If you are working with the JESS Parent Database the name is JPD c The program cannot find the above files anywhere else on the computer system This may be because the files are not where they should be or because a system specific mechanism needed to access them is not operational In particular a file called ELEMNT with extension USE or U is generally required It must be available in the JESS directory folder called VEWDTA On many computer systems the thermodynamic data files listed in b above will also be located in this VEWDTA directory folder instead of
51. e program requests confirmation of this Simply pressing ENTERI to implement the default Yes response causes the program to halt VIEW All the details in the database associated with each reference can be easily displayed The View command enables you to select references by specifying their identifier You may supply either the reference string in full or abbreviated or its unique number If you do not know the reference well enough to identify it in one or other of these ways you will need to find it using the Locate command described later on When you are finished with VIEW type Q for Quit to return to the JLR command prompt Literature Reference System 5 Reference Identification All references are specified in the following way The name of the publication is placed first followed by acomma The publication named may be either a book or a journal periodical the name may itself contain embedded commas and it may be abbreviated as described later The year of publication is placed next either in full e g 1950 or just as the last two digits e g 50 For a book this is all that need be specified For a chapter in a book a comma is appended followed by the chapter s first page number For a journal article the volume number and first page are appended separated by commas The volume field but not the page field may be null Spaces around the year volume and page are not necessary and if present are ignored Exam
52. ed from xqt by a space STRUCTURING YOUR DATA It is difficult to overstate the importance of properly organizing data on computers This very much applies to your JESS data where you ll find that all the thought and care that you put into establishing a system will be amply rewarded in the long run Individual requirements differ considerably so we cannot recommend a single approach that will suit everyone However you should think in terms of the number of projects in which speciation calculations may be required and the number of different contexts within each project that you may wish to model It is generally wise to structure your data accordingly having a separate directory folder for each project and separate sub directories for each major kind of model Disk capacity is cheap enough so you generally should not worry about a proliferation of stored models Much more critical will be your ability to organise them and name their storage places meaningfully If you are a beginner you should simply create a single directory space folder in which you can practice It is a relatively simple matter to start each modelling exercise from scratch by deleting the files created previously On the other hand when you get going in a serious vein you ll find that there are considerable advantages in preserving the data created during your modelling for future reference Text Editing 1 TEXT EDITING This document outlines what you need to kno
53. edundancies or inconsistencies and without any transformation of the data 2 The procedure involves many independent computer programs 3 Reactions and their equilibrium constants are represented in different ways at different stages in the procedure The transformations to achieve this are carried out automatically 4 The effects of kinetics on equilibrium calculations metastability in particular are more easily handled and are kept explicit 5 Theoretical corrections for changes in ionic strength and temperature are minimized The semi empirical functions used for such purposes are also known to work reliably for many types of reaction and over wide ranges of conditions temperatures up to 250 C and ionic strengths up to 5 M however errors in the available thermodynamic data are often limiting so it is important to control their propagation as much as possible 6 Large numbers of equilibrium calculations can be conveniently performed e g as required in the production of graphical output or in kinetic simulations You need to understand these issues to some extent at least to appreciate what JESS does You will encounter them shortly after you commence using JESS for modelling purposes They are likely to prompt you to ask the following kinds of question Modelling Facilities 3 Why do redundant inconsistent and incorrect data appear in the JESS Parent Database In compiling any database that is thermodynamically co
54. efault command i e it is selected simply by pressing the ENTERI key Generally when the execution of a command is completed or is terminated prematurely by you the program will re issue the prompt indicating that it awaits new data You can return to the JTH Command prompt by entering Quit or Q at any time The Thermodynamic Database 10 COMMANDS HELP This causes the program to display the list of valid commands and a brief explanation The facility is only an aide memoire QUIT This tells the program that you wish to terminate the present session The program requests confirmation of this Simply pressing ENTERI to implement the default Yes response causes the program to halt VIEW You may select one of four basic data types I O symbols All symbols can be scanned if you press ENTERI at the I O symbol prompt Alternatively you may enter a particular symbol or abbreviation The symbols displayed will begin with the one entered if a match is found You can then display subsequent symbols by repeatedly pressing IENTERI Species All data associated with a species such as charge molecular formula and names are displayed Reactions A reaction may be entered either as a number or as the complete reaction discussed previously The reaction itself in full JESS syntax is displayed as well as constants estimated at selected conditions of temperature and ionic strength Data The reaction itself and all data as
55. enholme and J Knight eds p 15 in his discussion of a model of biological control mechanisms On reflection it will be evident that a good simplification is a big advantage as a matter of fact it is a precondition for a model being at all serviceable If a map included all the details really present it would be quite useless The purpose of building models then is not to mimic nature perfectly but rather to enable useful thinking about the system of interest Modelling is at its most powerful when asking the questions What happens if and What are the major factors affecting We construct models because they help us to define our problems organize our thoughts understand our data communicate and test that understanding and only finally to make quantitative predictions Modelling Facilities 10 THE MODELLING Predictions are very difficult particularly about the future Niels Bohr cited by J Bruno in Modelling in Aquatic Chemistry p 612 Equilibrium Calculations 1 EQUILIBRIUM CALCULATIONS This document outlines briefly how you perform equilibrium calculations using JESS Read it carefully before trying to use any of the JESS modelling programs Only the practical procedures which you follow to obtain a speciation distribution are dealt with here it is assumed that you understand the reasons for these procedures given in detail in the MODELLING FACILITIES document
56. ermodynamics is the only physical theory of universal content which I am convinced The JESS Thermodynamic Database system called JTH provides a powerful and versatile means of storing and retrieving the thermodynamic data associated with chemical reactions Data in the JESS Parent Database provides the backbone for equilibrium calculations and thus for the determination of speciation This database has the three letter identification JPD Alternatively if you are working with a JESS equilibrium model the database is usually called DBA will never be overthrown Albert Einstein 1959 Initially you may feel that JTH databases are somewhat more involved than those of certain other programs for chemical speciation modelling It is therefore important for you also to be aware of the advantages of the approach that has been adopted Above all these advantages are directed to the vital needs of chemical modellers Indeed the structure of JTH databases and the JTH facilities for manipulating thermodynamic data are key mechanisms by which JESS aims to model chemical systems rigorously but yet conveniently Of most significance JTH does not require the chemical equilibria to be represented in a pre determined form Reactions are described entirely generally without classification of species either as complexes and components or as metal ions and ligands There is thus no restriction on the kind of chemical reaction that can be inc
57. gly we as the developers of JESS make the following plea Please take a while at least an hour to peruse this Primer thoroughly Find somewhere quiet Browse through each of the documents Get a feel for the system overall Establish where the detailed information is provided so that you can find it quickly when you need it Then and only then try out some JESS programs Also it is advisable to follow the sequence given in this Primer you will need to be familiar with all the early concepts when you begin modelling in earnest Hence skipping over them now only means you will probably learn about them the hard way We have done our best to keep the JESS interface straightforward consistent and convenient However the kinds of tasks we are concerned with cannot be reduced to a trivial operation So you need to be patient learn the rules which are not that numerous and practice following them Approaching JESS 4 We believe that you will then familiarise yourself with the JESS system best by using it Accordingly a basic approach is adopted in this Primer for each JESS facility that is described First we give you a worked example and then we provide the essence of what you need to make the facility work Details are largely passed over More comprehensive information appears in the interactive help facility and on the website see below which you should fully consult for further guidance once you have worked your way through this
58. h are the least well characterised but they serve to warn you about any unreliability of in the data available for your purposes This stage has the abbreviation LGK Determining species basis sets BAS stage Once a consistent set of reactions has been established and the relative thermodynamic stabilities of all species are fixed JESS can identify what are known as the basis sets of chemical species for your modelling calculations Mathematically elements of a set that can be combined to form all the other remaining elements in the set are known as a basis Chemically you can think of the basis species as components of your system from which all the complexes can then be formed by linear combination You should note however that with some basis sets the relationship may be difficult to see In general especially initially you should simply accept the basis species which JESS selects by default The stage in which the basis species for modelling are determined has the abbreviation BAS Note that it is also at the BAS stage that you can impose kinetic constraints on your equilibrium calculations This is done by re assigning appropriate sets of species from a specified thermodynamic basis species to a species which you want to become a basis species in your modelling calculations The effect is to express reactions for all the species in the set you specify in terms of the new BAS stage basis species instead of the previous LGK s
59. h as follows Modelling Facilities 9 The art of scientific modelling is finding the right questions to the answers not being afraid to make assumptions getting something from nothing e e e e how you do it not what you do All but the most trivial of equilibrium calculations entail a vast amount of information In modelling particular equilibrium systems you seek to understand how the chemical relationships express themselves in a given context You try to understand the trends involved and to establish whether there are any unexpected trends Indeed this is necessary not only to extend your knowledge of the system but also to verify the equilibrium calculation Modellers are often warned that the results of computer models are only as good as the input the dictum of Garbage in Garbage out Whenever this is said the emphasis is being placed on the final single definitive answer rather than on what can be learned along the way In fact one often cannot answer the specific question being asked but by finding the right questions to the information one has one can frequently make considerable progress This is in accord with Tukey s principle cited in the document on APPROACHING JESS at the beginning of this Primer Those who criticize models on the grounds that equilibrium calculations cannot do justice to the complexity of nature are referred to the words of Iversen Homeostatic Regulators 1969 G E W Wolst
60. he programs other than commands can also often be abbreviated Sometimes this involves methods of abbreviation which are more complicated than simple truncation The Literature Reference programs employ this kind of special convention as described later on The most important thing for you to remember at this stage is the Quit command Use this to terminate whatever you are doing In other words Quit can be entered in response to almost any prompt regardless of what the program is expecting The only significant exception to this rule involves the End command which is used to terminate some input sequences If you are at the top level of command of a program Quit will stop execution usually after the program has confirmed that you really do want to finish If you are at a lower level of program input Quit will return you to a higher level of operation Note that accordingly entering multiple Quit commands in succession will usually lead to program termination whatever your current status in the program You should also note that there two kinds of general assistance available to you when you execute any interactive JESS program Entering two question marks at any prompt will tell you the kind of information which is expected by the program Many prompts also provide detailed information in response to the Help command The commands Quit End and Help can always be entered as just Q E or H respectively Getting Started 3 ON LINE DO
61. hermodynamic result The abbreviation QED thus appears in some important JESS contexts You activate the calculation of a quasi equilibrium distribution by uncoupling appropriate reactions In effect this imposes a kinetic constraint on the chemical system by removing the connection between species by which elements in those species could otherwise be exchanged Further details on how to put all this into effect are given in the EQUILIBRIUM CALCULATIONS document under the section Determining species basis sets BAS Stage Why are the JESS corrections for ionic strength and temperature so complicated The complication is more apparent than real The thermodynamic parameters in a JESS database span a variety of conditions including values for different solvents background electrolytes ionic strengths and temperatures This is unlike other computer codes for performing equilibrium calculations that reduce all the available data to a single value at a particular reference state Hence JESS can employ values directly that happen to be measured under the conditions of your model Where these exact conditions are missing JESS can use values under conditions as close as possible Errors arising from imperfect methods of correction such as Debye Huckel functions are thus minimized For reasons of both simplicity and speed of calculation however it would be highly undesirable for JESS to select the values of thermodynamic constant
62. hich data are available including a summary of the ranges of pressure temperature and concentration and the number of data points View data for a ternary solution FIZ Command C H L Q S U V W lt L gt V Solute s lt Na 1 Cl 1 Mg 2 Cl 1 gt Physicochemical Property AC gt Mean Activity Coefficient Subject lt Na 1 Cl 1 gt Na 1 Cl 1 A subject is required for some physicochemical properties see the bolded entries in the table of properties in this document In the case of mean activity coefficients the property values refer to only one solute For this example either Na 1 Cl 1 or Mg 2 Cl 1 can be specified After entering the limits of temperature pressure and concentration the relevant data will be listed BACKGROUND INFORMATION Solutes The Physicochemical Property Database 5 Electrolyte solutes are denoted by Cation Anion where the cation and anion names have the same form as recognised by JPD The following cations are allowed H 1 Li 1 Bu4N 1 Al 3 Cu 2 Fe 2 Ni 2 Ag 1 Sm 3 Eu 3 The following anions are allowed OH 1 NO3 1 Acetic 1 C103 1 Formic 1 Mo04 2 Phthalic 2 AsQ3 3 Succinic 2 The allowed non electrolytes are H2 g SO2 g Sucrose Ethanol Na 1 K 1 Rb 1 Ba 2 Cd 2 Ca 2 Fe 3 La 3 Pb 2 Sr 2 Pr4N 1 Tl 1 Gd 3 Sc 3 Y 3 F 1 Cl 1 ClO4 1 SCN 1 Al 3_OH 1 4 AsO4 3 CrO4 2 CN 1 H 1_CO3 2 H 1_S0O4 2 H 1_P0O4 3 Oxalic 2 P207 4 SiH204 2 203 2 Oxine 1 H 1_Succinic 2 Ma
63. ich FMTJLR uses to prepare its output involve a number of conventions which you must be familiar with before you try to use the program The details of this are given in the User s Manual It is also possible to transfer literature references between databases This is accomplished by the programs PUTJLR to export the information creating a sequential file of data and GETJLR to import data from such a sequential file Literature Reference System 10 File Management 1 FILE MANAGEMENT This document outlines what you need to know about managing your computer files before you perform a JESS equilibrium calculation You ll need to be familiar with the details provided here when you start your chemical modelling For various reasons it is desirable to put the data needed for your modelling into your Once upon a time own area or directory separate from the the value of a program main JESS databases Most importantly this used to be proportional gives you freedom in carrying out your to the weight of its output calculations but there are other advantages as well such as speeding up your work and Nowadays the problem is how to isolating the JESS databases from the manage the infoglut vagaries of particular models and modellers Inevitably though there is a price to pay for this autonomy It is in essence that you must learn to manipulate your own data This means familiarizing yourself with the operat
64. ilities Initial Estimates and Use results of previous run Equilibrium Calculations 8 To illustrate how you should proceed in practice consider the first stage SUB You start by entering the information that defines the chemical system you wish to model This is accomplished by program TELSUB which you execute in the usual way For example Execute program TELSUB It should respond as follows TELSUB Version 8 2 Licensee Murdoch University Welcome Wednesday 17 Jul 13 15 50 This message only appears on the Creating Resident Data lt ___ __ first occasion i e when your working directory is empty Project lt New Project A gt My Project SUB Command H M Q V lt M gt M MODIFY 1 Chemical Elements 2 Primitive Species 3 Advanced Facilities Select one 1 3 lt 1 gt 1 You will then find that you are in a jed editing environment and can make whatever changes to the lists of first chemical elements and secondly chemical species that you require Remember that you terminate your editing of a list with the command Quit which can be abbreviated to Q This will return you to the Select prompt Create a list of appropriate chemical elements under option 1 You must include H and O these being the elements of water You should include any other elements that occur in the chemical system of interest to you except that C for carbon refers here only to inorganic species su
65. ill not be able to execute jed again until they have been deleted This is a mechanism to protect against the loss of data which may occur if there is a system failure during a prolonged editing session but it is not something you need be concerned with as a beginner A BEGINNER S GUIDE TO JED JED the JESS Editor is a simple line oriented facility for creating and modifying files The following description briefly covers the basic operations which are available to you Consult the JESS Users manual for a fuller account Activate the editor by typing after the operating system prompt here indicated as jed The program will display a welcome message and then prompt for the name of your file For example enter File try Please note that under the rules for JESS filenames certain restrictions apply here e g casing is insignificant the name must begin with a letter and must comprise 1 6 alphanumeric characters Only certain file name extensions are permitted examples of some full JESS filenames are msg wrk data est report txt under some operating systems only the first letter of the extension is used by the operating system If the file try wrk exists jed will load it into a working buffer and initiate its line editing mode if not an empty buffer will be created and your editing session will commence in input mode as described on the next page All editing changes are made to the buffer i e none are actua
66. ing system of your computer and learning how to manage the many files which are produced by JESS when an equilibrium calculation is performed BASIC OPERATING SYSTEM COMMANDS You do not need an advanced knowledge of your computer s operating system but you must at least be able to perform the following basic operations set up anew subdirectory UNIX mkdir DOS md VMS cre dir e move around your directory structure UNIX cd DOS cd VMS set default e copy files UNIX cp DOS copy VMS copy e delete files UNIX rm DOS del VMS delete Beginners should also familiarize themselves with the use of wildcard commands as soon as possible These can save a lot of time and help to prevent errors File Management 2 CONVENIENT JESS ABBREVIATIONS A standard set of three letter abbreviations exists for users of JESS under all operating systems These should have been set up as part of the JESS installation procedure The abbreviations are for standard commands you can enter at the operating system prompt i e not whilst a JESS program is running You should try several of the commands to test that the JESS environment has been activated on your computer They are as follows dir list files in your current directory jed activate the JESS editor shd show current default working directory shq show file quota if applicable xqt execute JESS program the program name is specified separat
67. invoke the View option and then enters say 1 for the first reference Thereafter one simply enters gt to display subsequent references Literature Reference System 4 USING PROGRAM VEWJLR This program provides the so called read only facilities of the JLR package i e it enables you to examine and to search for references but not to do anything that alters the database The program is command driven meaning that it expects you to enter one of several instructions indicating what you wish to do The prompt which is displayed when the program is waiting for one of these commands looks like this JLR Command H L Q V lt V gt In response you can choose to enter any of the commands discussed below Each of them can be shortened to their initial letter The letter shown on the prompt between angle brackets which during the session is usually the previous command entered is the default command i e it is selected simply by pressing the ENTERI key Generally when the execution of a command is completed or is terminated prematurely by you the program will re issue the JLR Command prompt indicating that it awaits a new instruction Otherwise you can return to the JLR Command prompt by entering Quit or Q at any time COMMANDS HELP This causes the program to display the list of valid commands The facility is only an aide memoire QUIT This tells the program that you wish to terminate the present session Th
68. ion of Zinc II has the symbol Zn 2 in which conventionally the element s chemical abbreviation is followed by the ion s signed electronic charge When entering JTH symbols you can in general truncate them The programs will request clarification if this creates an ambiguity Symbols like Zn 2 are called primitive to indicate that they are a basic building block of the database For convenience it is also possible to describe species in terms of combinations of primitive symbols In such cases the symbol is referred to as a composite In constructing a composite symbol you simply append the appropriate primitive symbols together separating them from one another with underscore characters _ The Thermodynamic Database 7 Chemical reactions Chemical reactions can be described using these species symbols Reactions can be written in any form just as long as the principles of conservation of mass and charge are obeyed In other words the JTH database does not impose constraints on which species are formulated as reactants and which as products Reactions are represented in much the same way as they are in ordinary chemical writing i e the symbols of the reactant species appear on the left hand side of an equals sign and the symbols of the products appear on the right hand side Species on the same side of the equation are usually separated from one another by plus signs but minus is also acceptable if that happens to be
69. l this of course is that it requires you to have a good feeling for data fitting and model selection procedures TROUBLE SHOOTING Although we have put considerable effort into the development of the JESS interface trying to make it as easy to use as possible our experience is that newcomers often encounter significant difficulties Should this happen to you be consoled that you are in good company We have identified two main reasons why these problems occur First and foremost new users run into difficulties because they are not familiar enough with the basic conventions of JESS These conventions are relatively few but nevertheless require some time and effort to learn For example you must be familiar with the ways of JTH our Equilibrium Calculations 11 thermodynamic database sub system and of JED our general text editor before you plunge into the GEM stages to tackle an equilibrium calculation Despite our best efforts to keep everything as simple as possible we have found that chemical speciation calculations and consequently the interface needed to deal with them cannot be reduced to triviality On the other hand we find that once familiar with JESS most users come to regard it as a straightforward and convenient tool The second difficulty experienced by new JESS users is of a more fundamental nature This concerns the occasional failure to converge of program DOQED when developing a new model The reasons for this an
70. lations should be performed Some aspects of this should be apparent to you immediately Although JESS is not a conventional expert system there is much similarity because its knowledge takes the form of explicit rules fuzzy logic and even some Bayesian type functions These decision making techniques assist you with tasks that require considerable expertise and which otherwise can prove difficult to accomplish without error Our overriding objective in the development of JESS has been to facilitate rigorous modelling of chemical speciation in complex environments Specific advantages as we see them are described in detail elsewhere e g in the documents on MODELLING FACILITIES and EQUILIBRIUM CALCULATIONS towards the end of this Primer Here it suffices to say that the JESS databases are much more comprehensive than those of other modelling packages and at the same time we feel are better suited to the requirements of modellers than are the standard literature sources of thermodynamic data Approaching JESS 2 Of course much still remains to be done It seems that full automation of chemical speciation calculations is still a long way off You still need to make a significant investment of time and effort in order to use JESS effectively However in the spirit of the quotation from Cardinal Newman at the front of this Primer we hope that even at the present stage of its development you will find JESS to be a powerful tool that can greatly
71. ling Everything that needs to be done to yield a speciation distribution and to formulate the kind of output you require is included The QED stage is the one that actually performs the equilibrium calculation The stages before this one prepare the input for QED Creating a sub database SUB stage To begin you specify the chemical elements and or JTH species symbols that occur in the chemical system you wish to model The system then extracts relevant information from the main JESS database shared by all users and creates a sub database for your particular application This sub database and all the files subsequently created are stored in your own directory folder i e individual area on the computer This stage is identified by the three letter abbreviation SUB Specifying ranges of conditions LGK stage Next you specify the conditions which are most applicable to your modelling This determines various priorities used by JESS and in particular influences which thermodynamic data are selected for your calculations JESS then calculates the relative thermodynamic stabilities of all possible species relative to a particular set of species known as the thermodynamic basis set You can check the output to see whether there are serious inconsistencies in the database for reactions involved in the chemical system you are modelling Such inconsistencies have no effect on your calculations because JESS ignores those reactions whic
72. lly performed on the file itself until the editing session terminates which means that your original file cannot easily be destroyed if the system crashes during the editing session Text Editing 3 JED operates in three main modes l Text accepting or Input Mode This is indicated by the prompt Input Every line is entered directly into the working buffer as you type it Terminate input by typing E for End as the only input to the prompt 2 Line editing mode This is indicated by numbers displayed in front of the lines shown on the VDU screen immediately above the Jed gt prompt You can relocate yourself in the file by entering any line number You can display a range of lines by entering two line numbers separated by a colon You can display all the lines in your file by entering where the period stands for the first line and the asterisk stands for the last e Enter a period to move to the first line of the file enter an asterisk to move to the last line in the file press ENTERI to move to the next line in the file if there is one Enter the command H for Help to obtain a summary of the Jed command set The following are those with which you should first familiarize yourself Advance or A display the next screenful of lines Back or B move backward one line Copy or C copy current line Delete or D delete current line Input or I enter Text accepting o
73. lonic 2 O2 g N2 g H2S g NH3 g Mannitol Sorbitol Glycerol Cs 1 Cr 2 Mg 2 U02 2 Ce 3 H 1_NH3 Me4N 1 Et4N 1 Cr4 3 Be 2 Zn 2 Pr 3 Br 1 CO3 2 B OH 4 1 Cr207 2 103 1 Mn0O4 1 CF3S03 1 Fe 2_CN 1 6 H 1_Malonic 2 CO2 g Hg g Xylitol Co 2 Mn 2 Th 4 Ti02 2 Co 3 Hg 2 Nd 3 I 1 S04 2 BrO3 1 H 1 2 _PO4 3 NO2 1 PO4 3 Propanoic 1 Fe 3_CN 1 6 Benzoic 1 H202 g Glucose Urea The Physicochemical Property Database 6 Physicochemical properties Properties are generally designated by 2 letter codes The property names and their codes are Property Name Unit ID Mean Activity Coefficient unitless AC Single Ion Activity Coefficient unitless AI Mean Activity Coefficient Ratio unitless AR Water Activity unitless AW Boiling Point Elevation C BE Boiling Point C BP Isobaric Molar Solution Heat Capacity J K mol CI Apparent Molar Heat Capacity Cp J K mol CP Volumetric Heat Capacity Quotient J K cm3 CQ Specific Heat J K g CS Apparent Molar Heat Capacity Cv J K mol CV Standard Molar Heat Capacity Offset J K mol CZ Absolute Density g cm3 DA Relative Density Difference g cm3 DD Specific Gravity unitless DQ Apparent Molar Expansivity KK EM Expansivity KK EX Freezing Point Depression C FD Freezing Point C FP Molar Excess Gibbs Energy kJ mol GX Standard Molar Gibbs Energy Offset kJ mol GZ Apparent Molar Relative Enthalpy kJ mol HA Apparent Molar Enthalpy of Dilution kJ mol HD
74. luded in the database However of particular import it means that information can be represented in the database as closely as possible to the way it appears in the primary literature So the need to transform chemical equilibria and their associated thermodynamic parameters is largely avoided The introduction of errors is thereby greatly reduced Further details are given in the MODELLING FACILITIES document of this Primer In addition JTH enables many equilibrium constant values to be associated with each reaction By weighting every value individually the database can thus aspire to be both critical and comprehensive There are many other benefits including a a more practical approach for dealing with changes in conditions such as temperature and ionic strength and b a more objective method of reconciling the marked differences that often occur between published parameters from independent investigators The Thermodynamic Database 2 A WORKED EXAMPLE FExecute program VEWSTH It should respond as follows VEWSTH Version 8 2 Licensee Murdoch University Welcome Wednesday 17 Jul 13 15 50 Enter the database name For example Use DBA instead of JPD JTH Database name JPD P for the database that is used for modelling purposes Begin by viewing some data JTH Command H L Q V lt V gt V View Data Reaction Species or I O symbol lt D gt S Species e g Na 1_Cl 1 H 1 This should evoke a display
75. ly thank those who employ us we trust JESS will reward their foresight and patience in supporting such a long term project Numerous discussions with colleagues have been invaluable in fine tuning JESS philosophy and improving the documentation And finally of course a particular word of appreciation to all who have assisted with the actual development of code or the entry of data The following need to be mentioned individually Peter Cardy Ria Jooste David Liles Ruth May Julius Pretorius Marita Roos Andrew Stanley Grahame Strong Peter Verhoeven Peter Wade Kris Parker and Khin Than Aye Disclaimer Whilst considerable effort is made to ensure that JESS is error free and user friendly we give no warranties JESS is made available to you on an as is basis under the condition that you use it entirely at your own risk Performance may not meet specifications interfaces may change in future No person or agency involved in JESS development assumes any responsibility for losses incurred through the use of JESS or of its documentation Consult the JESS Licence Agreement reproduced at the end of this Primer for details DOCUMENTS IN THIS PRIMER DOCUMENT 1 APPROACHING JESS DOCUMENT 2 GETTING STARTED DOCUMENT 3 THE THERMODYNAMIC DATABASE DOCUMENT 4 THE LITERATURE REFERENCE SYSTEM DOCUMENT 5 FILE MANAGEMENT DOCUMENT 6 TEXT EDITING DOCUMENT 7 MODELLING FACILITIES DOCUMENT 8 EQUILIBRIUM CALCULATIONS DOCUMENT 9 WHER
76. n density used to convert concentration units generally at room temperature The FIZ quantities refer to the solution density DA the velocity of sound SV and the isentropic compressibility under the specified conditions
77. not mean that you have to learn dozens of commands The commands used throughout JESS are consistent so once learnt they apply in much the same context when using other programs JESS always attempts to protect you from yourself The programs examine your responses and do their best to diagnose any errors you might make So don t be too concerned about making mistakes Don t worry be happy JESS prompts normally end with a colon though a question mark is also sometimes used If your VDU cursor is positioned just to the right of such a prompt the program is waiting for you to respond Anything you then type is only implemented when the ENTERI key is pressed Generally this allows you to correct typing mistakes quite easily provided they are deleted before you press the ENTERI key In an attempt to reduce the amount you have to do JESS will often display a so called default response at the end of a prompt enclosed within lt and gt characters Just pressing the ENTERI key will then impose this default as your response If the default is unsuitable you simply type the correct response instead As noted above JESS programs are command driven i e you choose from a set of commands to tell JESS what to do These commands can normally be abbreviated i e truncated Usually the first letter of the command will be unique and therefore sufficient Commands can generally be entered in upper or lower case Data required by t
78. note that no changes made to the sub database take effect unless the UCCs Unconditional Correction Coefficients in the database are also appropriately updated This is normally accomplished very easily execute program UPDUCC immediately after you have completed making the modifications with program UPDJTH Alternatively you can optimise the UCCs from withing UPDJTH Modify command option 7 In some cases however the automatic procedures performed by UPDUCC and or UPDJTH will not be adequate In particular this may occur when the new data you introduce are very different from those for that particular reaction previously found in JPD This is because UPDUCC does not in general change the set of UCC parameters used to fit the reaction s experimental data So for example if new data at finite ionic strength are entered for a reaction that only used to have data at infinite dilution your new data may not be automatically take into account in subsequent equilibrium calculations when ionic strength corrections are required Instead you must do the necessary yourself using programs EVEUCC and LODUCC The latter provide all the flexibility needed to optimise any desired set of UCC parameters EVEUCC does the calculation interactively and once you are satisfied with it allows you to write the result to an external file usually called EVEUCC WRK The data in this file are then loaded into your sub database by program LODUCC The downside of al
79. nsistent it is necessary to make a large number of assumptions about the purpose of the intended equilibrium calculation These assumptions relate not only to the domain of the model i e the range of conditions which determine the suitability of data and influence their selection but also to the appropriateness of some of the chemical relationships Typically literature data are transformed to accord with some pre determined set of components Unfortunately these choices are frequently arbitrary and inevitably they restrict the type of calculation for which the database will be suitable A major problem is that early on these assumptions tend to be rather poorly formulated and later on they tend to get forgotten By including data in the Parent Database exactly as it appears in the literature warts and all JESS retains flexibility The processes by which consistency is achieved are automated and thus remain under your control In particular this gives JESS models a unique reproducibility as well as allowing you readily to explore the consequences of different choices of criteria The approach also makes errors easier to avoid and easier to detect A major part of the work done for equilibrium modelling purposes by JESS arises directly from the need to sort out incompatibilities in the literature data and then to select thermodynamic constants using a well defined algorithm This is the price that has to be paid to avoid the error
80. ntering A A K K will permit you to specify two authors and two keywords The references then displayed will be those associated with both authors and the first keyword except that if any are also associated with the second keyword they will be excluded i e not displayed References can be shown in full using the same display as the View Command or in brief In the latter case only the reference identifier and its unique number are seen To prevent information scrolling off the top of the VDU screen the program interrupts the display of references requesting you to press ENTERI when you are ready to continue Actually you have three options i press IENTER to have the next reference or references displayed ii type Quit to abort the search or ii type a year of publication thereby causing the program to skip over references until the search reaches one published in the given year In the latter case note that since the references are output in reverse chronological order entering a year later than that of the last displayed reference has no effect and entering a year prior to the earliest reference located by the search causes the display to terminate i e a return to the JLR command prompt Authors Most references have an associated list of authors Each name is stored by the JLR system individually By convention you specify author names according to the following format i Family names are placed first suitably capitalised
81. odelling project Things should not be multiplied without good reason William of Occam 14 century philosopher What Next 1 WHAT NEXT The programs described so far in this Primer are perhaps the most important in the JESS package but they are only a few amongst some 350 Clearly there are many applications of JESS beyond those dealt with here Anyone who sits at the bottom of a well to contemplate the sky Th f this d t is to outli e purpose of this document is to outline eae eas some of the key remaining capabilities of JESS By far the most numerous are the various facilities for code development We obviously need many low level modules for testing purposes and there is a large suite of programs to assist in producing JESS on a variety of hardware platforms However three other categories of JESS program are probably of greater interest to you Han Yu 768 824 cited by J M Lehn Nobel Lecture 1988 PHYSICOCHEMICAL PROPERTY MODELLING AND DATABASES Characterisation of bulk aqueous solution thermodynamics as opposed to models of chemical speciation at the molecular level allows many physicochemical properties to be calculated with reasonable accuracy for most simple electrolyte systems Quantities such as activity coefficients osmotic coefficients relative enthalpies heat capacities and densities volumes are often useful in engineering environmental biological and medical applications A
82. of the hydrogen ion species Note the kind of information which is stored charge CAS registry number molecular formula molecular weight chemical names etc Species Q JTH Command H L Q V lt V gt V View Data Reaction Species or I O_symbol lt S gt D Reaction 1 This should evoke a display of the thermodynamic data available for the dissociation constants of water By convention this reaction is entered first Note that there are values for the equilibrium constant in log form lgK and for AH dH under various conditions of background medium temperature and ionic strength The reference numbers refer to the associated literature reference database The Thermodynamic Database 3 Try entering the same reaction in full form Reaction H 1 OH 1 H20 Spacing is important capitalisation is not Blank spaces must surround the equals sign and the plus sign which separates H 1 and OH 1 No spaces should appear in the species symbols H 1 OH 1 and H20 Now try another reaction To illustrate this consider say the formation of an ML complex by nickel II and glycinate The symbols for these species are Ni 2 and Gly 1 respectively The following illustrates two quick methods for specifying this reaction Reaction B130 Symbol for M metal ion Ni 2 Symbol for L primary ligand Gly 1 This should show the program analysing the symbols you have entered and locating them assuming
83. on the kind of information which you want from the calculation and the format in which it should be produced This stage has the abbreviation OUT What happens at each stage For various important reasons every one of the above GEM stages is subdivided into several distinct operations Each of these operations is accomplished by a separate JESS computer program The first of these programs allows you to enter information i e data and or instructions for that stage Sometimes this information is essential but often it is simply to change the decisions which are otherwise made by JESS The second of these programs actually performs the task described above for the stage in question With most of the GEM stages a third program also exists to provide output including a statement of the methods and assumptions that were employed in the calculations for that stage We use a consistent set of prefixes for the various types of computer program at each stage The programs by which you specify input interactively have the prefix TEL those that carry out the stage s operation have the prefix DO and those that are used to inspect the output of the stage have the prefix VEW Thus the full name of each computer program comprises one of these prefixes appended by the three letter abbreviation of the GEM stage itself A few of the GEM stages also have special facilities for printing their results The programs for this have the prefix PRT A summary of
84. ples of valid journal names are given later Examples of typical reference identifiers are The Double Helix 1961 dt book Physiological Chemistry 1976 157 lt q chapter Nature 1953 171 737 lt lt _ article Report No EPA 600 3 86 023 1986 lt __ report Summer Comput Simul Conf Proc 1984 563 lt ___ contribution in conference proceedings Note that journal part issue numbers are usually redundant and so are generally omitted However they may sometimes appear in parentheses following the volume number LOCATE The Locate command enables you to search for those references in the database associated with particular publications authors keywords or cross references Once you enter the Locate Command you will be asked about the type of search you require You can then enter one of the permitted codes A for authors K for keywords P for publications C or R for a cross reference Q to abort the search or H for some limited help Once the kind of search is established the program will prompt for the particular author keyword etc All references which have been entered with that item will then be located Literature Reference System 6 You can also Locate references which satisfy a combination of criteria You do this when prompted for Type of Search A K P C H Q by entering more than one of the codes A K P or C separated by or Here means include and means exclude For example E
85. potassium chloride solutions from 10 to 20 C in the concentration range up to 3 mol kg Note the kind of information which is stored property value concentration of the solute as published concentration in molality JLR reference number etc Press IENTERI when More is onscreen to view more database records or type Q to return to the main prompt FIZ Command C H L Q S U V W lt V gt U Solute s lt K 1 Cl 1 gt Mg 2 NO3 1 Physicochemical Property VM gt Apparent Molar Volume Lower temperature C lt 0 0 gt 25 Upper temperature C lt 150 0 gt 25 The Physicochemical Property Database 4 Lower pressure bar lt 1 0 gt 1 Upper pressure bar lt 4 76159 gt 1 Lower concentration m lt 0 0 gt Upper concentration m lt 17 3376 gt 4 Reference lt any gt This should evoke a display of the apparent molar volume values at 25 C including those that have been converted from related properties such as the absolute density Note that the values are converted to a common unit and the original property type is also shown Try locating information for a particular solute FIZ Command C H L Q S U V W lt V gt L Available options Search for Solute data Species data Physicochemical property data Reference data Solute symbols ARWN Select one 1 5 lt 1 gt 1 Solute s lt Na 1 Cl 1 gt Na 1 Cl 1 Mg 2 Cl 1 This should evoke a listing of the different properties for w
86. quations solved successfully Final sum of absolute equation values 1 05E 7 Number of iterations 5 Pre 1 bar Temp 25C Ionic Str 0 0M_ pH 7 00 pe 5 00 Eh 296mV VIEW 1 Speciation 2 Conditions Methods and Assumptions Select one 1 3 lt 1 gt 1 You may view the following at the current scan point Speciation of Specified Elements Speciation of Specified Primitives Total Proton or Electron Concentrations Individual Species Concentrations Phase Distribution of Specified Elements Saturation State of Solids Partial Pressure of Gases Charge Balance Ionic Strength Water Quality Indexes 10 Solution to Equations 10 Data Quality CHNIAKRWNS Select one 1 12 lt 1 gt 1 This leads to the display of the predominant species Specify that 5 the default are required Then specify the element calcium enter Ca Return to the main menu by entering Q for Quit Explore the output of VEWQED adventurously Terminate execution with Q for Quit at the QED Command prompt Clean up your directory folder Delete all files in your working directory folder immediately on exiting program VEWQED In other words be careful you do NOT move to another location and then delete everything there Equilibrium Calculations 4 THE GEM STAGES There are five essential steps in the sequence that comprises a JESS equilibrium calculation We call these the GEM stages GEM stands for Generalized Equilibrium Model
87. r Input mode Quit or Q terminate editing session View or V view a screenful of lines about the current line You can copy and delete a range of lines by following the command with two line numbers separated by a colon Insertions e g following the copy or Input commands are made immediately after the line at which you are currently positioned Text editing 4 You can edit individual lines to make minor changes using a set of special conventions based on characters typed immediately under the current line i a tilde causes the character above it to be deleted ii a circumflex a causes the character above it to be blanked out iii a solidus followed by some text causes the new text to be inserted in the above line immediately in front of the character above the solidus iv two consecutive soliduses Il causes the remainder of the line above to be deleted from the character above the first solidus If the two soliduses are followed by new text this is used to replace the text that is being deleted and v a backslash causes the casing of the letter above it to be changed i e uppercase to lowercase and vice versa Non alphabetic characters are unaffected You can find specified text in your file using the Locate command which can be abbreviated to L For example L label will search through the file from the first line to the last to find the first occurrence of the character
88. referred to as Na 1 Cl 1 and MgCl aq is referred to as Mg 2 Cl 1 Certain non electrolytes such as Glucose are also recognised Solution mixtures are specified by two solute symbols joined by with surrounding spaces For example the mixture NaCl KCl aq is given by Na 1 Cl 1 K 1 C1 1 The FIZ database stores physicochemical property values from the chemical literature Examples of the type of properties that are stored in the database include activity coefficients enthalpies heat capacities and densities Of particular note is that the database contains both values derived from experimental measurements that we call primary data and the results of models based on smoothing or regressing experimental information which we call secondary data Including both kinds of property values has a number of benefits especially for the purposes of characterizing solutions for which primary data are difficult to obtain from the literature whether due to age language or some other obstacle and identifying erroneous data All data in the FIZ database have been assessed and assigned weights based on their relative reliability Values that we reject are indicated by weight zero Other data are weighted on a scale from 1 low reliability to 9 highest reliability The Physicochemical Property Database 2 Information contained in the FIZ database can be inspected using program VEWFIZ An introduction to VEWFIZ and examples of it
89. s and hidden assumptions which are inevitable in the alternate approach i e transforming data during database compilation to accord with a pre determined modelling domain especially master species It is also worth focussing here on another advantage of the JESS methodology Bad values are intentionally included in the JESS Parent Database Although not of primary importance this is useful because less time gets wasted on constants in the literature that are hopelessly incorrect Otherwise if they are not properly recorded they tend to be re examined time and again JESS has a system in which all thermodynamic values are assessed during database compilation and assigned a weight These weights indicate our best assessment of the reliability of each value Every constant we consider worthless is given zero weight and thus has no influence on subsequent calculations Why does JESS initially require so little input from me To lighten things up we will start this explanation with some doggerel Even experts forget what once used to flow and can t well recall it given only a mo But YOU haven t a clue what you need to know and sure cannot learn it all in one go Banal as you may find this it succinctly describes two important pillars of JESS philosophy First as described above most equilibrium calculations depend on a large number of chemical and computational decisions Secondly you are unlikely to be
90. s begin again just by deleting your files and repeating the worked example from scratch Execute program TELSUB It should respond as follows TELSUB Version 8 2 Licensee Murdoch University Welcome Wednesday 17 Jul 13 15 50 This message only appears on Creating Resident Data lt the first occasion i e when your working directory folder is empty Immediately Quit the program Project title lt New Project A gt Q This sets up a default model for you involving a system of calcium carbonate equilibria You can see what has happened by entering the command dir at the operating system prompt to list all the files now present in your working directory folder You ll be pleased to know that you do not need to understand the file naming conventions nor are you likely to ever use them explicitly yourself Carefully and in sequence execute programs DOSUB DOLGK DOBAS and DOQED These programs transform the relevant thermodynamic data taken from the JESS Parent Database into the equations which are finally solved by DOQED Note the output produced by some of the programs as you go along but don t worry about what it means for the time being Execute program VEWQED It should respond as follows VEWQED Version 8 2 Licensee Murdoch University Welcome Friday 17 Jul 13 15 50 Project A New Project A Equilibrium Calculations 3 QED Command H Q V lt V gt V E
91. s being at thermodynamic equilibrium both for the purposes of calculation and behaving as such experimentally are actually not so Consider for example almost any organic complexing agent in a solution that is exposed to air From experience we know that such agents may interact with metal ions in perfect accordance with the law of mass action As long as the metal ions are not susceptible to oxidation this observation does not in general depend on how long the solution stands Yet there can be no doubt that many organics in contact with air are not in their most stable thermodynamic state Interestingly if the thermodynamic relationships describing such a system are properly established an equilibrium calculation will where it should show that CO2 g is formed by oxidation of the organic compound However most experts in speciation would not set up their calculation in this way They would be intent on describing the behaviour of the system in terms of changes in the metal ion binding say as a function of pH In other words the outcome of their equilibrium calculation depends on certain assumptions that they make wittingly or unwittingly about the kinetics of processes in their system This is not a trivial step to take The identical problem crops up in many other guises sometimes quite alarmingly For instance the question of how to simulate solutions containing ammonia and nitrate frequently arises for models of environmental in
92. s in the manner described above during the equilibrium calculation itself This is rather done beforehand saving time and possibly filespace JESS determines an empirical function to describe these values and employs this during its equilibrium calculations There are nine coefficients in the empirical function used by JESS we call these the Unconditional Correction Coefficients or UCCs You should note that our UCCs do not refer specifically to the range of conditions relevant to your modelling They are based on values from the database under all conditions for which the reaction has been characterised In this sense UCCs differ from the CCC functions used in earlier versions of JESS see May PM and Murray K Part II Talanta 1993 40 819 The current basis for UCCs has been described in the literature see May PM Chem Commun 2000 1265 Note Which particular reactions and hence which UCCs are ultimately used in an equilibrium calculation very much depends on the range of conditions under which the reaction has been characterised These are matched as closely as possible to the conditions of your model Modelling Facilities 7 EQUILIBRIUM CALCULATIONS Equilibrium calculations are often thought to be straightforward by those not closely enough concerned with them In fact many difficulties arise as discussed above These often confound even the experts in speciation and thermodynamic modelling see for example Part I May PM
93. s usage appear below It is also possible to display graphically key sets of FIZ data using an Excel spreadsheet and the so called 8 ball facility the latter being provided as an Excel macro within JESS Two examples of such graphs follow V em3 mol 1 1 2 p AC Li 1 Cl 1 p 1 bar t 25 C 0 8 0 6 0 4 p Iny FIZ all refs 0 2 Pitzer Auto 0 Hueckel Auto 0 2 0 4 0 6 k 0 8 0 1 2 a i i m mol kg 1 VM Na 1 SO4 2 p 1 bar t 25 C FIZ all refs Hueckel Auto Redlich Auto 0 1 2 3 4 5 6 m mol kg 1 The Physicochemical Property Database 3 A WORKED EXAMPLE Execute program VEWFIZ It should respond as follows VEWFIZ Version 8 2 JESS copyright C 1985 2014 Licensee Murdoch University Welcome Monday 10 Feb 14 14 49 FIZ3 is the largest FIZ FIZ3 is the active dataset ee dataset containing all the data available Begin by viewing some data FIZ Command C H L Q S U V W lt V gt V Solute s lt Na 1 Cl 1 gt K 1 Cl 1 Physicochemical Property OC gt Osmotic Coefficient Lower temperature C lt 0 0 gt 10 Upper temperature C lt 325 0 gt 20 Lower pressure bar lt 1 0 gt 1 Upper pressure bar lt 120 51 gt 1 Lower concentration m lt 1 0E 4 gt Upper concentration m lt 8 515 gt 3 Reference lt any gt This should evoke a display of values of the osmotic coefficient of aqueous
94. scover a need to modify things or to insert new information for your own particular purposes JESS has a large number of programs for these and associated tasks although whether you have access to these or not depends on your circumstances The most important program in this respect is UPDJTH This allows you to update any Thermodynamic database hence the abbreviation UPD The program facilitates the insertion of new thermodynamic data and it allows you to alter data if you have entered it incorrectly Of course to modify them you will need write access to the database files from the operating system of your computer Program GBLJTH is also used to modify data when certain systematic changes spanning multiple reactions need to be made Database modification introduces a need for so called housekeeping i e the internal tidying which becomes necessary to maintain access efficiency For this purpose programs such as BLDJTH MNTJTH and DMTJTH are provided The Thermodynamic Database 13 It is also likely that you will soon want to transfer data between databases This may be between your own personal sub databases or it may involve the exchange of data with other JESS users For example we strongly encourage you to send us newly measured equilibrium constants or other data which you feel is missing from the JESS Parent Database this should save you from having to re enter such data every time you receive a new version of the Paren
95. sociated with it are displayed Details are given in the JESS Users Manual The three character codes represent the techniques by which the constant and its error were obtained The numbers within square brackets are literature references you can obtain the full reference from the associated JLR database see THE LITERATURE REFERENCE SYSTEM which is documented in this Primer The Thermodynamic Database 11 LOCATE Select one of the following options At this stage you should ignore the others shown on the Locate menu e Reactions containing a given species Entering any species primitive or composite will result in ALL the reactions containing that species being displayed Note that some lists could be very long However they are shown one screenful at a time you can terminate the display by entering Q or Quit You can also search for reactions containing combinations of species To do this at the prompt enter your selected list with subsequent species separated from the one before it by a plus for inclusion or a minus for exclusion The plus and minus signs must have a blank space on either side e Primitive species containing a given element The symbols of all the primitive species containing the chemical element Fe N S you specify are displayed You can also search for primitive species containing combinations of elements As above separate the elements by or for inclusion or exclusion respectively e
96. t Database from us The programs used to exchange JTH data are called PUTJTH and GETJTH the former writes the data into a set of sequential computer files and the latter loads the information back into a database from such sequential file sets JESS also contains programs which check the integrity of your databases and yet others which can list selected information from your databases in various ways Full details on how to use these various programs are given in the on line documentation available through program HELPER Oa OO O amp O OO OOO OO OO OOO OS OOO OOO OO OOO OO OO OO OO 4 The JTH suite of programs is dedicated to Ruth May who with no formal training in chemistry learned what needed to be done and entered much of the data into the Jess Parent Database Sa OO Oe O amp O OO OO OS OOO OS OO OS OS OOO OOO OO OO OO OOO Oat Comments on compiling databases It can be verified from personal experience that it is a colossal undertaking to assemble a critically evaluated table of thermodynamic data for inorganic compounds Steven G Bratsch J Phys Chem Ref Data 89 18 1 Good nature and good sense must ever join To err is human to forgive divine Alexander Pope in Essay on Criticism cited by HC Helgeson Am J Sci 82 282 1143 The Thermodynamic Database 14 There are ancient cathedraly which apart from their cowsecrated purpose inspire solemnity and awe Evew the curious visitor speaky
97. tage basis species Program TELBAS can assist you with the decision making if your select the Uncoupled basis Species option under the Modify command Equilibrium Calculations 5 Performing a quasi equilibrium calculation QED stage At long last the stage is set to perform the actual equilibrium calculation itself In particular the equations of your model are now ready to be constructed These include but are not restricted to the mass balance equations from which the total concentrations of your system can be calculated by summing over all species Equations imposing the solubility products of solids in equilibrium with solution and equations describing various adsorption isotherms can also be introduced You must specify the necessary analytical concentrations of your system and the identity of any solids which are to be explicitly included in the calculation Solids may either be required to occur at equilibrium or allowed freely to precipitate and dissolve A convenient mechanism also exists for carrying out repetitive calculations in which for example particular concentration s are scanned over a given range The calculation of Ey vs pH plots or Pourbaix diagrams as they are often called is a common requirement For reasons which are outlined in the MODELLING FACILITIES document this stage in which the speciation distribution is determined has the abbreviation QED Producing output OUT stage Finally you must decide
98. terest Interconversion of the two substances occurs sometimes but not always Systems containing sulfide and sulfate provide another common example in the same vein There are also ligands with more than one kinetically distinct binding conformation such as thiocyanate in which the less thermodynamically favoured arrangement may persist long enough for an equilibrium to be characterized Likewise Ostwald s rule of stages in crystallization which holds that the least stable solid tends to precipitate first has far ranging implications for many speciation applications The rules Ralph shouted In each of the above cases different results You re breaking the rules will be obtained from an equilibrium calculation depending on how it is set up Who cares And since the way it should be set up in practice lies wholly outside the realm of Ralph summoned his wits thermodynamics there are no fundamental rules to guide how it should be done Because the rules are the only thing we ve got It follows that you will often want to perform equilibrium calculations in a way that Lord of the Flies reflects certain non thermodynamic by William Golding constraints on the system JESS will assist you to do this and keep track of what you ve done Modelling Facilities 6 We call the outcome of such calculations quasi equilibrium distributions to distinguish them from the rather rare true t
99. ters don t make misteaks Modelling Facilities 2 Significant progress has been made in the development of JESS since its inception in 1985 It has grown into a large software package with various advanced modelling facilities It is unlike any other computer code for equilibrium calculations Some of the more important differences are described below In general however JESS is very much concerned with the assumptions that such calculations always involve and how errors in thermodynamic data propagate This means that it exposes you to issues which are often otherwise concealed You will find that this is not always a comfortable experience You should thus regard JESS as a powerful research tool for investigating chemical speciation in complex environments rather than as just a means of obtaining equilibrium distributions If you have a single application as opposed to a broader interest in the computer simulation of equilibria in solution you should probably NOT attempt to use JESS yourself Ask one of us the JESS authors to help you The remainder of this document assumes that you are a determined practitioner of chemical speciation calculations or wish to become one VIVE LA DIFFERENCE The approach taken by JESS towards equilibrium modelling is distinctive in several major respects 1 Thermodynamic parameters appear in the database just as they appear in the literature i e generally in their raw form without omission of r
100. the basic methods for editing data You do not need to master all the facilities that are available but it would be unwise to proceed without being able to make simple changes with confidence In this respect practice makes perfect The easiest way to practice your editing skills is to use the JESS editor called jed Although you will not generally use the jed program itself during your modelling activities you will often find yourself in identical editing environments to those supported by jed You need to be able to recognize these various environments so that you can operate appropriately Text editing 2 A WORKED EXAMPLE You should begin by working in an empty directory space Using jed you should create a file with some arbitrary lines of text Then practice making a selection of changes Following the instructions below try to insert new lines of text copy and delete them also make some specific changes to existing lines of text without retyping the entire line You should take careful note of the three different modes of working which jed supports If anything goes wrong and you find yourself stuck simply delete all the files in your working directory and begin again This is the reason for practicing in an empty directory space to begin with Note in particular that if for some reason the temporary files created by jed called jed jnl and jed use are not deleted at the end of your editing session as they should be then you w
101. ting the one required For example the abbreviation EM would also match Experimental Methods Electrochemical Methods and Environmental Models So if this were entered the program would need to determine from you which particular keyword is intended Searching for items by abbreviation can be speeded up by supplying more lowercase letters For example if the JLR system contained many keywords beginning with E it might take significantly longer to locate Environmental Models if you entered the abbreviation EM rather than EnvM It is worthwhile taking a little time to familiarize yourself thoroughly with this abbreviation mechanism Once you are familiar with it you will find that it is a very convenient way of specifying information for the computer with a minimum number of keystrokes Literature Reference System 9 INFORMATION AT ANY TIME At odd times and places you may wish to check what publications authors or keywords exist in the database This can be done using the query facility Queries made in response to virtually any prompt take the form XXX abbreviation For example PUB Tal could be entered to ascertain whether the journal Talanta was in the database s list of publications The question mark occurring as the first character of the response signifies that a query is being made The letters XXX represent the kind of data item that is concerned this may be PUB for publications AUT for authors KEY for keywords and R
102. urray Insight Modelling Services Pretoria South Africa Primer Supplements Nda The Physicochemical Property Database 1 THE PHYSICOCHEMICAL PROPERTY DATABASE This document describes how to access the information in the JESS physicochemical property database The numerous facilities within JESS for processing such data are described elsewhere INTRODUCTION TO FIZ The JESS Physicochemical Property Database system called FIZ provides a means of storing and retrieving the physicochemical property data associated with aqueous binary one solute plus water and ternary two solutes plus water solutions Most of the data concern simple electrolyte solutions such as NaCl aq or KOH aq The general idea is to link the stored values for recognised solution properties to the particular bulk solute or solutes defining the solution and to the well defined composition temperature and pressure The greatest obstacle to discovery is not ignorance it is the illusion of knowledge Daniel Boorstin 12 Librarian of the United States Congress In most cases solutes are strong electrolytes Within FIZ electrolytes are specified by a combination of a cation and an anion in the form of their JPD symbols separated by a forward slash symbol Electrolytes are always assumed to be electroneutral in other words the stoichiometry of the two aqueous ionic species is determined implicitly For example NaCl aq is
103. vast number of experimental measurements and compilations of smoothed data have accordingly been published in the chemical literature We are endeavouring to capture these published values i e to extract them from their various sources and to store them in computer accessible form In addition to the data collection itself every value is assessed and where appropriate used to parameterise certain mathematical models In this way good descriptions of the thermodynamic behaviour for simple aqueous solutions can often be achieved The JESS database of physicochemical property values is called FIZ You can inspect these data using program VEWFIZ Program VEWFIZ allows you to see a the raw values and the corresponding literature reference s for a specified solute b unified values i e all represented in a standard common unit and c converted values for different but equivalent properties such as solution density and apparent molar volumes Note that JESS employs characteristic symbols to identify bulk solutes For example the FIZ symbol for sodium chloride is Na 1 Cl 1 This allows the electrolyte to be distinguished from the corresponding chemical species in solution whose symbol would be Na 1_Cl 1 Full documentation is available for the FIZ interface including lists of the recognised physicochemical properties and the available solutes with their respective symbols see program HELPER to locate this documentation What Next 2
104. ventional method of specifying reaction numbers without typing them out in full By entering certain special symbols the program can be made to display reactions on either side of the one last shown or to display the reaction last entered into the database The symbols are as follows Symbol Meanin lt Reaction number one less than that just shown gt Reaction number one more than that just shown The last reaction Using this mechanism you can easily and rapidly scan through a sequential series of reactions using just one keystroke to display each one Type V for View at the JTH Command prompt and then select D for Data Enter any reaction number from 1 to where is the total number of reactions in the database Thereafter you can simply enter either gt to display the next reaction and its data or lt to display the previous reaction Note that some reactions have more data than can be displayed on the screen at once The program will suspend output and display the prompt Continue lt Y gt You can have more of the data shown e g by pressing IENTERI or you can stop it by typing either N or Q BACKGROUND INFORMATION Chemical species The concept of a chemical species is fundamental to JTH It uses information about species to categorize all the thermodynamic data stored by it so you can easily locate things and to check your input Every species in the JTH database is represented by a symbol For example the
105. verlap FIZ has more flexibility regarding property types and units and it is better at dealing with two dimensional tables of data SOL has much greater flexibility regarding solution composition which is specified using JTH symbols The Solubility Database is still in an early stage of development To date coverage of the relevant literature remains modest containing only about 20 000 data values We hope to grow the database considerably over the next year or two The Physicochemical Property Database 2 A WORKED EXAMPLE Fxecute program VEWSOL It should respond as follows VEWSOL Version 8 2 JESS copyright C 1985 2014 Licensee Murdoch University Welcome Monday 10 Feb 14 13 48 Begin by searching for some data SOL Command H L Q S U V lt L gt Type of search E F K P R S H Q lt S gt K Keyword Gypsum This searches for all sets of data with Gypsum What sort of display as a word in their title Full lt Brief gt Quit Set Title 433 Calcium Sulfate Gypsum Solubility in H Lit C104 435 Calcium Sulfate Gypsum Solubility in MgCl2 436 Calcium Sulfate Gypsum Solubility in Na Mg Chloride 437 Calcium Sulfate Gypsum Solubility in Na Mg Chloride 445 Calcium Sulfate Gypsum Solubility in NaCl Soln 446 Calcium Sulfate Gypsum Solubility in NaCl Soln 447 Calcium Sulfate Gypsum Solubility in NaCl Soln 448 Calcium Sulfate Gypsum Solubility in H
106. w about editing text before you perform a JESS equilibrium calculation When you start your chemical modelling you ll need to be familiar with the editing conventions described here in order to control your calculations and to modify their input Practice yourself for MODIFYING DATA heaven s sake in little things and thence Although JESS attempts to make the proceed to the greater preparation of your input data as straightforward as possible through the use of menus and pre set sequences of prompts we Epictetus quoted by have learnt that there is a limit to the Donald Knuth in The Art of usefulness of such methods In particular Computer Programming when you need to modify your input data as opposed to preparing it initially there are just too many possibilities to deal with conveniently by question and answer For this reason we employ a mixed approach in which changes are made by you using a generalized editing facility as well as by providing appropriate responses to programmed questions and by selecting between available options How you go about making changes using the generalized editor is the subject of this section You will find the need arises in many different contexts within JESS Indeed we consider the widespread use of the same editing conventions throughout JESS as a key part of our development of a consistent and user friendly interface It follows that you should familiarize yourself with
107. y of more appropriate basis species by considering the pH and Eq of the solution Further information about this topic can be obtained using program HELPER MANAGING AND PRESERVING YOUR MODELLING SCENARIOS A key feature of JESS modelling design is that you develop each model in its own storage area directory or folder It is therefore quite easy to create use and retain separately your various modelling scenarios It is then clearly important to keep what you have done in a form that allows you to go back and see exactly why the results turned out as they did Every major modelling exercise requires too many chemical specifications and too many assumptions to be remembered and thus reproduced unfailingly On the other hand you will likely explore many possibilities so it is impractical to record absolutely everything To find a sensible balance you will need to be discerning well organised and above all good at record keeping Remember also that the JPD database continues to evolve so you cannot rely on it to provide exactly the same thermodynamic data as it did in an earlier Equilibrium Calculations 12 version of JESS This problem can be solved by preserving the DBA database in the directory folder that stores each modelling scenario However there is a danger is that the DBA database may get overwritten later on by program TELSUB You can guard against this possibility by copying DBA IND to DBB IND at the conclusion of your m

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